An Omega Among Alphas
by Lastsyns
Summary: For his entire life, the Doctor has been forced to take a pill that suppresses his Omega scent. Now trapped aboard the Valiant by the Master he knows it is only a matter of time before he is discovered.
1. Chapter 1

Throughout the long history of the universe, many societies were structured around Alphas. The Alphas became rulers while their beta counterparts took care of the day to day work. Then there were the Omegas. Omegas by nature were submissive to the Alphas. They were the ones who took care of the children, staying within the home all day. In every society but one, there was a mixture of males and females within every standing. That one society was the Time Lords. Long before most could remember, a great war took place between the Time Lords and a now extinct species. That species in order to halt the growth of the Time Lords, released a disease that caused the Time Lords to become barren. Left with no other options they began to loom all their children. The looming process though gave them a choice.

So the age of the Alpha males began. They were loomed to be stronger, smarter and faster than their female counterparts who were only loomed to be docile betas or omegas. No one knew for sure when they decided to no longer interact with the other societies. They turned their backs on the universe that still had alpha females and Omega males. A unanimous decision was made to watch the universe from afar, never interfering. That was until one child was born that would change it all.

This child was not loomed like the rest but born to a young mother. She had been told that she should terminate the pregnancy but refused as she saw her pregnancy as a blessing rather than the burden that others thought it was. She was stronger then most omegas and held her head high as they whispered around her about the imperfect child she was carrying. They didn't understand how she was happy not being able to choose the gender, hair color, eye color and traits of her child. The first body of the child set the standard for the rest.

On a cold night in the dead of winter, she gave birth to her son, alone in the barn outside of the large house that no longer felt like her home. Her beautiful Theta would see the stars shortly after his birth and grow to love them. He would return to the barn many nights over the next few years to hide and watch the stars. He never dreamed that one day he would be banished to the barn for a week at a time as his body went into heat. He had been told that all males were Alpha and shamed his family when he presented as an Omega. Even his mother who had wanted nothing but the best for her son looked down on him. She didn't fight when the council forced him to take a pill that hid his Omega scent and announced that he had presented as a beta. He never forgot the shame in her eyes as tears filled his eyes. He had failed his family yet again. He vowed that day that he would never let an Alpha claim him.

To keep from shaming his father further, he agreed to the arranged marriage that his father made. She was another Omega though and she never understood why he didn't try to claim her. He never told her and lived in shame as he raised their sons together. As time passed he realized that he wasn't happy. He couldn't remember the last time that he had felt alive and he thought of ending his life. Instead the first chance he got, he stole the TARDIS and took to the stars. Never to look back.

-DW-

The Doctor knelt on the cold floor of the Valiant. He was chained so that he had to keep his head up and his back straight or he risked breaking his neck. In front of him Jack was chained to the wall. Though they were alone at the moment, neither one of them risked speaking and bring the Master back into the room. He kept his eyes focused on the ground in front of him as he didn't dare look up at the naked Alpha. It had been over a month since they had been trapped on the Valiant by the Master. During that time, the Master had taken pleasure in tormenting his two captives. The Doctor shuddered to imagine though what was going to happen when his pill wore off. He had managed to suppress his Omega scent for almost 900 years and now he was going to be discovered.

Looking up he saw a young man approaching with food. The man knelt down in front of him and lifted up a small piece of bread. He eyed the bread wearily, but he was too hungry to resist. He ate it, groaning unhappily when he was only given less than half a slice of bread. The small amount of food made him feel hungrier than before and he regretted his decision to eat. As the man moved away from him he paused sniffing the air. Turning his head, he looked directly at the Doctor before sniffing the air again. The Doctor saw the realization cross the man's face.

"Please," The Doctor whispered as the man stood frozen.

"Are you an," The man began his voice just as low. The Doctor interrupted him before he could finish.

"No," The Doctor replied, his eyes wide with fear. The man nodded turning once more to leave. He came back a moment later with another small piece of bread. He knelt down in front of the Doctor and rather then offer him the bread the Doctor saw a tiny pill in his hand. He recognized it as the same one he took to suppress his scent. He knew it was a risk for the man to bring him the pill, but he was extremely grateful to have it. He opened his mouth allowing the man to place another piece of bread in it, the pill safely hidden inside. As the man left again, he noticed Jack was looking at him curiously. He didn't make eye contact with him as once again he turned his eyes to the floor.


	2. Chapter 2

For four months, the man helped the Doctor to keep his secret. The Doctor never knew why the man risked his life each month to slip the Doctor the pill that suppressed his scent. Living as an Omega in hiding though, the Doctor supposed it was because the man understood the struggle the Doctor had lived with. He wanted to tell the man not to continue bringing him the pill, but his own fear of what would happen if the Master found out his was an Omega stopped him. He instead gratefully took the pill each month as the man fed it to him along with whatever bit of food he had been allowed to bring from the kitchen that day. The Doctor was beginning to think that he would get through his ordeal with his secret intact. That was until a new man came from the kitchens. He couldn't trust this man with his secret so instead he waited, hoping the other would return.

He realized though that his hope was childish when he felt his body fast approaching heat. The pill was wearing off and with an Alpha constantly in his presences his body was reacting to the scent. He groaned trying to push himself as far away from Jack as possible, but the chains had little to no give. He kept his eyes to the ground as he tried to breathe normally and force his body to ignore the fact that there was an Alpha nearby. Even as a Time Lord he wasn't that strong though. He couldn't help the shudder of fear that went through him as he heard Jack sniffing the air. He lifted his eyes slightly to see Jack looking at him with a perplexed look on his face. He adverted his eyes once more. He tried not to keep track of the minutes that passed until he heard the door to the room open once more. He didn't look up as he heard footsteps approaching him, but the growl from Jack told him it was another Alpha.

"Well, well, well, what do we have here?" The Master wondered as he came closer to the Doctor. The Doctor couldn't help the trembling as the Master knelt down in front of him. He gagged as the Master licked the side of his neck. "Oh Theta, you never told me you were an Omega."

"I'm not," The Doctor said firmly. He could hear the fear in his voice though and even he didn't believe the words that came out of his mouth. He felt the Master reach behind him, unhooking the chains that held him in place.

"You can't hide your scent from me. The stench of Omega is all over you. Though I wonder who was giving you the pills to suppress your scent all these months. Once I claim you, you will tell me and then I will have them put to death," The Master informed him.

"Please don't do this Koschi," The Doctor begged.

"Leave him alone," Jack snapped angerly. He was just as surprised to find out that the Doctor was an Omega but forcefully claiming him had never crossed Jack's mind. Perhaps it was because Jack was raised in a different time that he never saw an Omega as someone you could claim. He had watched his own parents interact and they had a partnership where his mother submitted to his father by choice. He had always wanted that type of relationship and never took an Omega who felt they had to be a slave. There was also the fact that every Omega who had been forcefully claimed broke. He couldn't watch that happen to the Doctor as, even though, the Doctor was strong eventually the abuse would wear him down too. He had seen it too many times where an Omega became shells of their former selves at the hands of an Alpha.

"You can't stop me," The Master hissed at Jack. The Doctor looked at Jack with fear in his eyes as the Master pulled him closer. "Theta is mine."

"He is not a trophy and I won't have you destroy everything I love about the Doctor," Jack yelled at him. He pulled on the chains as hard as he could as the Master moved behind the Doctor. He heard a click and felt the chains loosen. Turning his head slightly, he saw a guard slip the key back into his pocket. Jack smiled at him. Some of the guards aboard the Valiant were horrible to them, but a few resisted. This one had loosened the chains before for Jack so that his feet would touch the floor when the Master had him hoisted up. He was stupid for letting Jack go and the choice may cost him his life though. Jack was too focused on the Doctor to care at the moment. He felt the hair on the back of his neck stand up as he moved closer to the pair.

"I said leave him alone," He growled. Out of the corner of his eyes, he saw several of the guards raise their guns at him. He didn't fear them or his own death if it meant the Doctor was safe.

"Leave him," The Master stated standing up. He moved so that he was in front of the Doctor as the men lowered their guns. The Doctor scrambled backward away from the two alphas. He wanted to run, but there was no way out of the room except past the guards. Jack was right he wasn't a trophy, he was the Doctor and had been raised to be an Alpha. He didn't dare to step between the Alphas though as he didn't match their strength. He couldn't stop the Alphas from fighting each other though the thought of either of them claiming him made his feel sick.

"I won't let you claim him," Jack hissed moving closer.

"Then stop me," The Master replied.


	3. Chapter 3

Jack and the Master circled each other slowly. Jack knew he was stronger than the Master but all it took was just one gesture and the guards watching the fight would step in. Within a matter of seconds, Jack could be dead. That didn't stop him though. Glancing over, Jack saw the Doctor watching them wearily. Whoever won the fight would win the right to claim him. Jack wouldn't let that happen. Without any further thought, Jack lunged at the Master. The Master easily moved out of Jack's way. Jack turned, swinging his fist. The Mast ducked out of the way, turning into Jack and hitting him hard on the back. As Jack bent forward he was kicked hard in the stomach causing him to gasp for breath. He jumped quickly back to his feet, moving back a Jack was stronger, the Master was more agile and Jack wasn't going to win this fight by strength alone. He had to rethink his strategy.

"I don't think he really wants to win," The Master taunted as he moved slowly to the left. Jack copied his movements but heading to the right, circling as he waited for the Master's next move. He didn't have to wait long as the Master tried once again to use his agility to out maneuver Jack. Jack was ready for him this time and as the Master came at him, he turned into the Master. Using his leg, he knocked the Master off of his feet and down to the ground. Jack was immediately on top of him. Swinging he connected firmly with the Master's jaw. He swung again as pain ripped through his side and the buzzing of the laser screwdriver filled the air. He screamed in frustration and grabbed the screwdriver out of the Master's hand. Without looking he threw it behind him. That was just the opportunity the Master needed though and with Jack distracted he hit him with the side of his hand in his throat. Jack grabbed at his throat as the Master pushed him off.

"I am going to make you watch me claim him," The Master said, kicking Jack in the stomach once more. "I am going to chain you to the wall and make him beg you for help as I claim his body as my own." Jack didn't even think about it as he grabbed the Master's foot in his hand as the Master kicked again. He pulled the Master's feet out from under him, causing the man to hit the ground hard. Within moments, he was on top of the Master again, hitting him. He kept swinging, feeling his fist connect with the Master's face.

"Jack stop," The Doctor cried out as he watched the Masters face turning black and blue with each punch. Blood was pouring from the Master's nose and he had a cut above his eye. Jack paused as he looked up at the Doctor. Grabbing the Master's shirt, he pulled it, causing it to rip. He tore the shirt off of the Master's chest before standing up. Grabbing the Master, he rolled the man as he forced his hand behind his back. He tied a quick knot around his hand, then grabbed the other one and tied it in place.

"I win," Jack huffed as he stood up.

"Then claim him," The Master yelled as he fought against the restraints. Jack went over to the Doctor. The Doctor trembled as Jack leaned over him. He closed his eyes, waiting for the pain that didn't come.

"No," Jack replied. Instead, he felt hands gently pick him up. He clung to Jack's chest as Jack turned towards the tent that he called his home.

"This isn't over unless you claim him," The Master screamed. Jack ignored him as he took the Doctor inside of the tent laying him down on the single blanket he was given. Not touching the Doctor anymore, he stepped outside of the tent closing it.

"I am not going to claim him and neither are you. You lost your right to claim him and the only reason I haven't killed you is he told me to stop. Touch him again though and I won't hesitate to kill you," Jack informed the Master. The Master nodded at one of his men and Jack heard the sound of a gun before his world went dark.

Gasping in the precious first breath of life, he opened his eyes to find that he was once more chained to the wall in the conference room. Guards were standing at the door and the Master was nowhere to be seen. Turning his head as far as he could, he looked towards the Doctor's tent. The tent was open a crack and he could see the Doctor curled up beneath the blanket. His eyes were closed and his chest was rising and falling steadily as he slept.

"Don't worry the Master didn't touch him," The guard who had freed him stated. Jack turned his attention to the man. He was surprised the man wasn't dead yet but had no doubt that he would be soon.

"What happened?" Jack wondered.

"After he had you killed, he tried but we all saw the fight. He had you chained up again and stormed out of the conference room," The guard told Jack.

"This isn't over. He is going to try again. I don't understand why you are risking your life to stop him," Jack informed the man.

"I had a sister who was claimed by an Alpha. She ended up killing herself a few years later. I vowed that I wouldn't let that happen to another Omega and I can guarantee you a lot of the men here think the same way, that is the problem when you hire betas out of fear that an Alpha is going to overthrow you," The man chuckled. Jack smiled at him, the man was right. Alphas constantly fought, so it was dangerous to have groups of them working in the same place. Men who were weaker Alphas would often hire Betas instead. The problem with Betas were they were unpredictable. They could be as docile as an Omega or as strong as an Alpha.

"Be careful," Jack told him.

"My life is going to be over soon anyways, at least I can make a difference while I am alive," The guard told Jack. He liked the young man, but he was right. The Master was going to kill him first chance he got. For now though at least Jack could rest knowing the Doctor was safe.


	4. Chapter 4

For almost three days, there was no sign of the Master. Though Jack was still cautious about what the man might be planning, he was relieved to have the break. He was still chained to the wall in the corner and under strict orders not to be let down. The Doctor on the other hand had free will to roam the conference room. Jack watched on as the Doctor explored the room he had been held captive in for four months. He looked through paperwork, licked numerous objects or just relished in the fact that he could stretch out in his tent without being beat. Jack's favorite moments though were when the Doctor would come sit at his feet, enjoying the feel of the Alpha's skin against his back. Even if he wouldn't admit it, being an omega made him crave the Alpha's touch and he went to Jack for it. He was sitting near Jack when the door opened on the third day and the Master entered with a large smile on his face. Jack immediately tensed with worry, but the Doctor looked at and then disregarded the Master.

"And here I thought we were friends," The Master pretended to pout over the Doctor's attitude. "I even have a surprise for you." The Doctor shuddered slightly, moving slightly behind Jack's legs. One thing he knew for sure is that he wouldn't like any surprise the Master might have.

"You have no friends," Jack snapped at him.

"And here I was going to let you down. Oh well, I guess you will just have to watch from there," The Master taunted.

"Watch what?" Jack wondered.

"All in good time Jackieboy. First we need to wait for our other guest," The Master answered as he sat down in the chair at the head of the conference table. The door opened again and Jack watched as the Jones family was lead into the room. Clive stopped and sniffed the air in confusion for a moment before turning to look at the Doctor. He could clearly smell the Omega male even with his Omega wife and beta daughter with him. Jack didn't fear that Clive would try to claim the Doctor, but he still growled a slight warning.

"We're all here!" The Master said excitedly as he ignored Jack's growl. "Gather round. You to Doctor. I don't want you to miss this." The Master moved to the window making sure that the Jones family followed him. The Doctor stood but hesitated, looking to Jack. Jack nodded and the Doctor slunk slowly over to the group. Looking out the window he could just barely see the outline of land below them. He narrowed his eyes in confusion as he tried to figure out what the Master was planning.

"After Jackieboy beat me, I thought you all could use a reminder on who is in charge here. It took a few days of searching, but I finally got confirmation that Martha is in Japan. I never really did like Japan. Did you Doctor?" The Master asked. The Doctor turned to look at him. As he did the ground below them lit up as flames engulfed the land. They were too far up to hear the explosions, but they could see the devastation as the flames spread.

"Why?" The Doctor asked as he finally found his voice

"I warned them not to help Martha. Now everyone in Japan is going to pay for harboring her," The Master seethed.

"You can't do that," The Doctor argued. He cried out as the Master's hand connected with the side of his face, knocking him to the ground.

"You forget your place Theta. I am going to remind you of it though." He motioned to the door and ten guards entered. They pointed their guns at Jack while several more came in and unchained him from the wall. Jack fought them as they drug him out of the conference room.

"Where are you taking him?" The Doctor wondered as he watched.

"Somewhere you can't find him," The Master replied. The Doctor cried out again as two more men grabbed him, hauling him to his feet. The Master stepped forward and grabbed the Doctor's chin. He held it tightly in his hand as he looked him in the eyes. "I think you will find Theta, that I always win."

The Doctor was taken out of the room and down a flight of stairs. He walked beside the men as they went down a long hallway to a single windowless door. One of the men stepped forward and opened the door to reveal a room no bigger than a closet. The Doctor was pushed into the room and the door closed leaving him in overwhelming darkness.


	5. Chapter 5

If there was one thing that the universe was in a general agreement about, it was that it was cruel to lock up an Omega that was in heat. Granted it was still a practice that was many species did, but it was usually for the Omega's benefit to keep them from being claimed and bred. There were also cases like with the Doctor, where the Omega was locked up to hide the family's shame. It didn't surprise him that the Master knew he was going into heat. As an Alpha, he would have been able to smell the pheromone changes before the heat actually set in. It also explained why he had been locked up away from Jack. In a way, he was relieved because once his heat fully set in he could end up doing something undignified, like humping Jack's leg. The thought mortified him enough that he curled up in the dark closet thankful to be alone.

He didn't like the pitch darkness though. The dark was something that he had feared since childhood. He had grown up learning to tolerate it, but in the closet there was no light seeping through from the hall. He was completely alone in the dark. He shuddered, closing his eyes against the overwhelming darkness that threatened to pull him under and tried to rest.

When he opened his eyes again, he was still in the closet. His body was burning up and he was sweating profusely. He whimpered as he curled up tighter into himself, trying to ignore his aching body. It was no use though. Even if Jack never properly claimed him, Jack was still his Alpha. His body wanted the Alpha to claim him and breed him. He started to snake his hand downwards to relieve the tension but stopped himself before he actually reached his groin. He was a Time Lord and better than that. He didn't need to touch himself to feel any relief. He couldn't rest though. Couldn't settle down. In the dark closet, he squirmed and writhed, trying to find any relief possible. For two days, he suffered alone until the door of the closet finally opened. He blinked up into the blinding light to see several betas standing there.

"Here. Take this," One of them said softly. The man leaned down and handed him a bottle of water. He took it from him gratefully. The water was still cool and he gulped the bottle down quickly.

"Thank you," He told them after finishing the water. He stood up on shaky legs. None of the beta's helping him or touching him.

"Come with us," The man said. He nodded and followed them down the hall. He realized they were heading to the conference room as they walked and he stopped in fear. He didn't want to be claimed, even if his body did. He just wanted to go back to the closet and hide until his heat was over. One of the guards put a hand on his shoulder to push him forward and he whimpered.

"Don't touch him," The first man snapped. The second guard removed his hand and stepped back once more. "I know you don't want to go in there Doctor but we are under strict orders from the Master to bring you. Please just come with us."

"Alright," The Doctor agreed and followed them once more. He didn't want anyone else to die because he didn't listen to the Master. As they reached the conference room the guards took places outside of the doors and the Doctor walked in. Upon entering he froze, regretting his decision. He had expected Jack and the Master to be in the conference room, and while they were there, there was also three other Alphas including Clive. All of them looked over when the Doctor entered, his heat calling them to mate with him. The door of the conference room slammed shut, trapping him inside. His blood ran colder as he backed away from the Alphas.

"Mine," Jack growled at them, moving between the Doctor and the others. The two new Alphas puffed up their chest at Jack, ready to fight him for the right to claim the Doctor. The Master moved to join the two and Clive went to stand with Jack. The Doctor on the other hand tried to get as far away as possible from the Alphas. He knew why the Master had brought the other's in and he didn't like it. Since the Master had lost against Jack the first time, he couldn't keep his dignity and challenge Jack again. By bringing the other Alphas in, he avoided directly challenging Jack but was still able to fight for his right to claim the Omega once more. He hadn't counted on Clive taking Jack's side though. Clive was a mated Alpha and, therefore, better able to keep his head when there was an Omega around.

The Doctor made it up the stairs of the conference room and into the corner of the room away from the fight. Down below him he could hear the screams of frustration and pain as the five Alphas fought for the right to claim him. He tucked himself back behind a desk, curling as small as he could as he tried not to listen to the fight. It seemed as it went on for hours before the sound of footsteps approaching filled the air. He heard a man sniffing and then the footsteps got closer. He cried out in surprise and fear as the desk suddenly shifted, revealing his hiding place. He looked up to see Jack standing there. He was naked like usual and his body was covered in cuts and bruises.

"Please, Jack. Don't do this," The Doctor begged as he fought against the instinct to roll over and present himself to the winning Alpha. Jack stared down at him, his eyes wide and pupil's dilated. Jack curled his hands into fist, digging his fingernails into his palms. He concentrated on the pain he felt in his hands, trying to fight his instincts as well.

"Run," Jack whispered, his voice hoarse. The Doctor didn't hesitate as he stood and ran down the stairs. He tried not to look at the men laying on the floor of the conference room. The two Alphas who had been brought in were dead and Clive was slumped against the wall breathing evenly. He didn't see the Master at first but heard the chains rattle in the corner. Looking over he could see the Master had been chained up in Jack's normal spot. He kept running though. Grabbing the doors, he flung them open and was immediately greeted by guns.

"Take me back to the closet," He told the men. The men didn't respond, except to raise their guns higher.

"Do it," The Master moaned.

"Come with us," One of the guards stated. Relieved the Doctor followed them away from the conference room and to the safety of the closet.


	6. Chapter 6

The Doctor spent the rest of his heat miserable inside of the closet. The only thing he was thankful for was the fact that he was away from Alphas who wanted to claim his body as their own. By the time, his heat was over he was tired, thirsty and miserable. He just wanted to sleep and recover, but that wasn't going to be the case. Soon after his heat ended the door to the closet opened once more and several beta guards stood outside of it. He was pulled to his feet, but he found it hard to stand on them. The guards didn't care as they drug him down the hallway and to a bathroom. There was a shower against the back wall and they deposited him in it before all but one guard stepped out.

"You have ten minutes to wash the scent of you heat off of yourself or we will do it for you," The guard told him. Not wasting any time he turned the shower on and reveled in the feel of the water against his skin. He cupped his hands under the cool water, drinking his fill. He would probably regret it later but at the moment he didn't care, Jack would protect him. The thought should have made him laugh as the Master was the one holding them hostage, but he was an Omega regardless of whether or not he wanted to be. He couldn't help but think like one sometimes, especially when he didn't have his pills. The pills stopped his Omega hormones from taking over his body and allowed him to pretend he was a beta. Right now though he hadn't had his pill in over a month and the Omega side was winning once more and his omega side was telling him that Jack was his Alpha and the Master meant nothing.

He quickly showered, not because the Master wanted him too, but because he wanted to look nice for Jack. Turning off the water was a signal for the guards to return. One of them handed him a towel and he dried himself off as the man watched on. He handed the towel back to the guard and the guard threw it to the side before reaching into his pocket.

"Take this," The guard demanded, offering the Doctor the Omega suppressant pill. The Doctor was surprised to see it. He reached out and took the pill in his hand.

"The Master doesn't want me to go into heat again," The Doctor mumbled to himself. He glared at the guard as he was slapped across the face.

"Don't talk, just take the pill like you are told," The guard spat. The Doctor looked the guard straight in the eye as he put the pill in his mouth. Holding it under his tongue he swallowed. "Follow me," The guard told him, turning to lead him out of the room. As he did the Doctor wiped his mouth with his hand, removing the pill. As they walked by the sink, he dropped it down the drain. He tried not to smile to himself as he followed the guard out of the bathroom and down the hall to the conference room.

Walking into the conference room, he found the Master sitting at the head of the table drinking a cup of tea. Jack was tied to the table in the room and where his body wasn't black and blue, was covered in cuts. The Jones family was also in the room, standing in Jack's normal corner. They all looked frightened and the Doctor hoped silently that they weren't forced to watch the Master torture Jack.

"Ah Theta, you are just in time," The Master announced happily. He motioned to the chair next to him and the Doctor walked over to it, reluctantly sitting down. "I hope you enjoyed your heat."

"I've had worse," The Doctor told him truthfully.

"And the guards gave you your pill?" The Master questioned.

"Yes," The Doctor answered.

"Good, good. You can understand why I can't have you going into heat again. You shouldn't have to suffer when your Alpha is tied up," The Master chuckled as he tried and failed to sound sympathetic. The Doctor didn't answer as he looked Jack briefly in the eyes. Whether or not Jack even registered he was there was unclear as Jack's breath was becoming more labored. The Doctor knew he was going to die soon and there was nothing he could do to stop it. Still his Alpha would return to him because unlike the Master, Jack wouldn't stay dead. "Now on to business."

"Which is?" The Doctor questioned.

"I've tolerated your mouth up until now Theta. Don't make me punish you," The Master hissed softly. The Doctor closed his mouth and sucked in his lips. The Master smiled at him before turning to address the Jones family.

"The three of you have lived here by my good graces as your daughter and son have wrecked havoc below. I found Martha last week in Japan and now I am happy to tell you that we have found Leo," The Master informed them.

"No," Francine cried out moving forward.

"Control your omega or I will," The Master hissed at Clive. Clive grabbed Francine's arm gently, pulling her back.

"Now as I was saying. We have found Leo. His family has already been disposed of but I thought you should witness his execution," The Master sounded almost gleeful at the suggestion. He hit a button and a screen lowered from the ceiling.

"Don't do this," The Doctor whispered.

"That is one Theta. Open your mouth again and I will make Tish suffer the punishments instead," The Master growled. The Doctor closed his mouth, looking at Jack again as he took his last breath, his body going still. It was fascinating to watch as his body rapidly healed itself using the atron energy. He watched until Jack took a deep breath in, signaling his return to life.

"Good now that we are all here," The Master cheerfully stated. He pushed a chair into the middle of the room where he had a good view of the screen. One of the guards brought him a bag of popcorn and he sat back on it as the events unfolded in front of them. Jack put his hand on the Doctor's shoulder, trying to comfort him, but there was no comfort to be found as the Doctor was forced to watch the Jones family lose another child.

"We will stop him," Jack whispered in his ear. The Doctor just nodded. It had been a week now since he was able to connect with the network due to his heat. Focusing his attention once more on it, he prayed that Martha was still alive spreading the message. If not the few people she reached would have to be enough.


	7. Chapter 7

The Doctor barely registered when the Master stood, applauding the images that were on the screen. He acted as though he had just seen a fantastic show then witness the grisly execution of a man. The Jones Family huddled together in the corner, traumatized from the images they had been forced to watch. Leo had suffered terribly for hours at the blades of the Toclafane before he finally succumbed to his injuries. The Master didn't give the family anytime to grieve as guards grabbed each of the family members, dragging them apart.

"Leave them alone," Clive screamed as Tish held onto him for as long as possible.

"Daddy," Tish cried out as her arm was wrenched of Clive's hands with a sickening snap. She screamed in pain, but the guard offered her no sympathy as he continued to follow the Master's orders.

"Now why would I do that?" The Master questioned Clive. Clive was chained in the corner as Francine, and Tish were removed from the room. The Master paid Clive no more attention, but he wanted Clive to witness what was going to happen next. Sitting down next to the Doctor he placed a hand on his leg.

"Did you enjoy the show?" The Master asked him. The Doctor glared at him with all the hatred he could muster but didn't answer him. The Master squeezed the Doctor's leg, digging his fingernails in deep as he stared him in the eyes.

"Yes," The Doctor hissed finally.

"Good. Now, I have been trying to convince Jack to relinquish his right to claim you as his Omega. Jackie boy is stubborn though and seems to think he has the right to be your Alpha even though he is nothing but a worthless ape. So I have come to the conclusion that the only way that he is going to give up his right to claim you is if you chose me as an Alpha instead," The Master explained.

"And why would I do that?" The Doctor asked. He gritted his teeth as the Master's nails went deeper into his leg.

"That is a very good question and one that I have thought long and hard about this last week. You have no reason to let me claim you, even though we are the last two of the Time Lords and our mating would mean the continuance of our species. You have no reason at all to bare my children though, but if you don't I am going to drop sweet little Tish out of an airlock," The Master sounded almost sympathetic, but the Doctor knew him too well. He could tell that the Master was enjoying himself. He narrowed his eyes further at the Master as he tried to ignore the pain in his leg. The Master snapped his fingers on his other hand and the screen turned on. On the screen, he could see Tish being held by one of the guards. Across from her Francine was staring at her.

"Let them go," Clive cried out.

"No," The Master answered.

"You can't force him to chose you. I beat you and won the right to be his Alpha," Jack argued the Master. The Master didn't hesitate before he pulled his gun out and shot Jack clean between the eyes. Jack's head fell to the table as his eyes glazed over. The Master put his gun away, turning his attention back to the Doctor.

"See first I will drop Tish, making her dear ole Mummy watch and if you still refuse, I will drop Francine next," The Master informed the Doctor as he finally released his leg. "I will give you one hour to think about it Theta."

"Go to hell," Clive yelled at the Master. The Master ignored him once more as he stood. He motioned to the guard though who hit Clive in the stomach with the butt of his gun, causing Clive to gag.

"Think about it carefully Theta," The Master whispered as he left the room. The Doctor sat quietly, staring at the fingernail imprints on his leg. The last thing he wanted was to have the Master as his Alpha, but he wasn't going to make the Jones suffer the loss of their only living child. He didn't need the full hour to decide. He was going to let the Master do something that no one else in 900 years had managed, he was going to let him claim his body. He looked over sadly as Jack gasped his first breath of life in.

"Don't do it," Jack begged the Doctor. The Doctor looked away.

"I have no choice Jack," He answered.

"There has to be another way to save Tish," Jack told him.

"There isn't," The Doctor answered. Standing up he started to head to the door of the conference room to let them know he wanted to speak to the Master.

"As your Alpha, I forbid it," Jack snipped at him angrily. The Doctor didn't stop though as he passed by Clive.

"Thank you," Clive whispered. The Doctor nodded once but kept going until he reached the door. He knocked on the door of the conference room and almost immediately it was opened by a guard. The guard aimed his gun at the Doctor, but the Doctor wasn't afraid of the man.

"Tell the Master I need to speak to him," The Doctor told the guard before turning around. The guard closed the door on him. The Doctor moved to the middle of the room and got down on his knees, putting his hands behind his back, he gripped his left wrist tightly in his right hand. As he sat back on his heels, he spread his legs slightly apart as he dropped his head so that his chin was touching his chest. Jack recognized the submissive stance immediately.

"Doctor," He began.

"No one else is going to die because of me Jack," The Doctor interrupted. The door to the room opened as Jack stared at the Doctor. The Master came in his face lighting up with happiness as he took in the Doctor's body.

"My body is yours to claim my Master," The Doctor told him. His words were without any emotion as he continued to stare downwards. Even if the Master claimed him, in his hears the Master would never be his true Alpha. Only Jack had that right and he had gained it without touching him.

"You always did know what I like Theta," He purred with happiness. Jack growled at him as he moved closer to the Doctor, stopping right in front of him. "Now get up and follow me."

"You can still change your mind," Jack begged as the Doctor rose to his feet. The Doctor didn't dare look over at Jack as he followed the Master to the door of the room.

"Release my daughter," Clive said before the door could close. The Master paused in his steps.

"After the Doctor has fulfilled his end of our deal, your daughter will be released to you," The Master agreed. Once more he left the conference room and as the door closed behind them, he heard Jack scream in frustration. Biting back his fear, the Doctor continued to follow his new Alpha.


	8. Chapter 8

The Doctor was lead down to a hallway he had never been to before. There was one single door at the end of the hallway and the Master went to it opening it up. Stepping inside after him, the Doctor saw it was a spacious bedroom. Laying on the white blankets on the bed, the Master's current Omega Lucy, was stretched out almost cat-like on the covers. She had been sleeping, but upon the Master's arrival woke up and slunk to the floor. She kneeled there waiting for the Master's orders.

"Out," The Master barked. The Doctor was slightly surprised, how gracefully she rose to her feet before heading to the door. She closed it behind her. The Doctor felt his hearts speed up as he was trapped alone in the room with the Master. He was doing this for Tish, he reminded himself but it didn't help. He was being forced to submit to an Alpha who only wanted to claim his body and didn't care who he hurt in the process. He could become pregnant with that Alpha's child as quickly as his next heat. He swallowed hard as he realized that he thrown the pill down the drain that could have prevented that for another month.

"Kneel," The Master hissed at him. Without thinking about it, he dropped to the same submissive pose that he had taken in the conference room. He lifted his eyes slightly as he heard the Master unbuckling his belt. "Eyes on the floor." The Doctor glared at the Master before lowering his eyes once more.

"It seems you have forgotten your place Omega. Years of acting like an Alpha has made you think that you can stand up to me. That ends now. I am going to teach you that you are no better than the worthless apes you have come to love." The Master circled around the Doctor so that he was no longer in view. "Move your hands forward." The Doctor did as he was told. He cried out in pain as the belt slapped against the bare skin of his back. "Count them."

"One," He replied.

"Try again," The Master said as the belt whistled through the air once more.

"One Master," The Doctor cried out.

"I think sir will work for now," The Master informed him. "Same count please."

"One sir." The amount of sarcasm the Doctor managed to put into the two words slightly amazed the Master, but he was in no mood for the Doctor's games at that moment.

"We can do this all day Theta. It isn't my back that will suffer," The Master informed the Doctor as he snapped the belt. "Again."

"One Sir," The Doctor said finally. The belt landed again without another comment and the Doctor continued the count. The game continued until he had to stop himself from moving at every lash and the count just became hollow words. He was drenched in sweat, but he didn't dare move his hand to wipe it away from his eyes. It was almost a relief when he heard the belt hit the floor as the Master dropped it.

"Get up on the bed," The Master told him. His blood ran cold and he slunk as slowly as he could towards it, hoping the Master would change his mind. The Master just watched him move. He sat down on the edge of it and the Master sighed. "Quit trying my patients Theta. On your knees, shoulders to the bed."

The Doctor rolled over into the degrading position, that put his bottom high in the air. The Master wasted no more time before moving behind him and pushing himself deep into his body. He gritted his teeth, holding the blankets tightly in his fist as he was taken roughly. The Master had no regards to him as he chased his own release, digging his fingers into the Doctor's bony hips. The Doctor tried to separate his mind from what was happening to his body but all he could think about was the feeling of the Master's clothes brushing against his skin and the pain that spread through his body. The Master found his release deep inside the Doctor. After he fell forward, laying across the Doctor's back, biting hard into his shoulder to claim him as his own. The Doctor didn't care about the consequences as he fell to his side after the Master moved away from him.

"Get up," The Master growled angrily. His whole body shaking he followed the Master's orders. The Master motioned for him to follow once more and he did. He kept his eyes on the ground as he was led back to the conference room. Jack was still tied to the table and Clive was in the corner of the room in the same position as well. Though he heard Jack gasp in horror as they entered the room, the Doctor didn't dare look at either of them.

"My daughter?" Clive questioned through gritted teeth.

"Will be returned to the kitchen for her nightly duties," The Master responded before turning to leave. Once he was gone the Doctor walked over to the table Jack was tied to.

"Doctor," Jack whispered as he began to pick at the first knot. He didn't care about the consequences as he began to pick apart the knots that held the ropes around Jack's wrist. His hands were shaking so badly though that he slipped and scratched Jack once or twice. "Sweetheart?" The Doctor didn't answer him, afraid to open his mouth. He got the first knot undone and Jack helped him with the next, followed by the ones around his ankles. Sliding off the table, he sat in one of the chairs by the table. The Doctor knelt down in front of him but still didn't say anything.

"Doctor, you're scaring me," Jack told him softly. He didn't reach out to touch the Omega that was in so much pain as he was now clearly marked as belonging to another Alpha. As an Alpha, he had been raised that you didn't touch a marked Omega unless given permission by their Alpha. He couldn't just let the Doctor suffer alone though, the Time Lord meant too much to him. Reaching out he put a hand on the Doctor's chin, lifting it so he could look into his terrified eyes. "Doctor?"

"I'm sorry I disobeyed you Alpha," The Doctor finally managed to stutter as tears broke free from his eyes. Jack stared at him. Though the Master had managed to claim the Doctor's body as his own, the Doctor's mind hadn't been broken.

"I forgive you," Jack answered softly. He didn't know what he expected to happen, but he was surprised as the Doctor moved, climbing up on his lap, curling as much as possible into his arms. Sobs wracked the Doctor's body as he gripped Jack's shirt tightly. Jack wrapped his own arms around the Doctor.

"I'm sorry, I'm sorry," The Doctor repeated over and over in between sobs. Jack gently nipped at the claiming mark on the Doctor's shoulder. The Doctor calmed down from the gentle bite and the warm body of his true Alpha. He went still and Jack released his shoulder, looking down into the sleepy eyes of his Omega.

"I love you," Jack whispered kissing him softly on the head. Picking the Doctor up, he carried him to the tent. Laying him down on the thin blanket, he curled his body around the Doctors, not wanting to be separated from him. He kissed the Doctor softly on the head once more and the Doctor sighed as he snuggled as close as he could get to his Alpha.

"Sleep now and when you wake up we'll figure this out," Jack told him. He didn't dare close his own eyes as he guarded his Omega and waited for the Master's return. He couldn't promise that the Master would never manipulate the situation to touch him again but as the Doctor's rightful Alpha, he could promise the Master would have a fight on his hands if he did.


	9. Chapter 9

After about an hour of laying with the Doctor on the hard floor of the conference room, Jack tried to stand up and stretch. The Doctor though whimpered and curled further in to Jack. Sighing Jack settled down again to hold the tramatized Time Lord. Pulling the thin blanket around the Doctor, he cocooned the Time Lord in it as he continued to to hold him.

"I've got you," Jack reassured the sleeping man as he dropped a kiss onto his head. The Doctor needed to sleep and heal his battered body. The evidence was clear that the claiming had been brutal from the whip marked back to the bruised hips. The bite mark on the Doctor's shoulder was deep and the Master's teeth had broken skin in some places. He was going to have a nasty bruise from it as well. Thinking about the Master, Jack wrapped himself tighter around his Omega. He was surprised the Master hadn't come back yet to gloat about claiming the Doctor but if he did, Jack was going to kill him. It didn't matter what the Doctor said, the Master's life was forfit as far as Jack was concerned.

"Does it always hurt?" The Doctor asked softly, startling Jack. He had thought the Doctor was still asleep. Looking down, he saw the Doctor's eyes were open a crack. They were red from crying and Jack gently kissed his head again before answering him.

"Not when a claiming is done properly," Jack answered, not wanting to lie to the Doctor.

"Will you claim me properly?" The Doctor wondered.

"Not right now sweetheart. I am not going to go anywhere though regardless of whether or not I claim your body. Now just close your eyes again and rest. Your body needs to heal," Jack whispered. The Doctor did as he was told. Reaching up Jack gently stroked the hair behind the Doctor's ear. He kept up the gentle movement until the Doctor's breathing evened out. After Jack was sure that he was asleep this time, he carefully got out of the tent.

"I think you should claim him," Clive spoke up from where he was still chained in the corner. Jack felt bad that they couldn't get Clive down as well but he didn't have the key to the chains.

"I don't want to hurt him anymore then he already has been," Jack responded.

"I don't know the Doctor that well. I only met him once we were brought aboard this ship and I have seen the strength that he possess. He stands up to the Master as though he really were an Alpha," Clive told Jack.

"I know. I am amazed he isn't but his scent doesn't lie," Jack replied. He wandered over to the table looking for left over popcorn or water or anything else he could use to take care of the Doctor.

"I saw his eyes today though when the Master brought him back into the room. I have seen that same look on other Omega's faces who have had their bodies used. If you don't claim him and the Master continues to, it is going to break him. Maybe not quickly because he is so strong but soon the Omega that you love will be replaced by a broken shell," Clive informed Jack. Jack stopped what he was doing and put both hands on the table hanging his head. He didn't want Clive to be right, but he had seen the look as well. The normally hyperactive Time Lord had all but cried himself to sleep. Jack wanted to be respectful of the Doctor and not claim his body. He was going to have to though, in order to save his mind. Turning around he walked back to the tent and laid down once more by the Doctor.

The Doctor slept for several hours and Jack let him. During that time, one of the other Omega's aboard the vessel brought them food and water. Word had spread quickly about what happened to the Doctor and the Omega had snuck Jack in extra water for the Doctor. Jack was grateful for it. After the Omega was gone he continued to hold the Doctor until he woke up on his own. He drank the water that was offered to him, but didn't touch the food.

"I've thought about your request," Jack told him.

"And," The Doctor wondered, looking up into Jack's eyes.

"I will claim you. If that is what you truly want," Jack replied softly.

"It is," The Doctor responded. He started to roll over onto his stomach, but Jack stopped him. He wasn't surprised the Doctor was moving to his hands and knees. The Master would have taken the Doctor in the most degrading way possible, but Jack wasn't going to do that to the Time Lord. Instead, he kissed the Doctor's softly as he laid him on his back.

He spent a long time making the Doctor forget that they were in a ratty old tent, with just a thin blanket. Jack knew that he should have hurried in case the Master showed up but Jack was not going to hurt the Doctor if he could help it. He ran his hands up and down the cool body, making the Doctor first relax and then moan under his touch. The Doctor's eyes still held fear as Jack positioned himself between his legs, but he was as gentle as possible as he entered the Doctor for the first time.

"It hurts," The Doctor whimpered as he clutched at Jack's bareback.

"I'm so sorry. I never wanted to hurt you," Jack whispered as he leaned forward and rest his forehead on the Doctors. The Doctor looked up into Jack's eyes as Jack held himself in the same position. "Do you trust me?"

"Yes," The Doctor answered. Jack held him as he began to move. Their joining was slow as Jack kissed the Doctor on the lips or just held himself up so he could stare in the Doctor's brown eyes. Jack found his release first deep inside the Doctor, but he made sure that the Doctor followed him over the edge. Pulling the Doctor tight to him he nipped the Doctor's shoulder with his teeth, right on the Master's mark, before moving off of him. He collapsed down on his back and the Doctor laid with his head on his chest.

"Well?" Jack wondered as he snuggled The Doctor to him. The Doctor's response was to kiss Jack on his chest as he closed his eyes. Smiling to himself, Jack let the Doctor drift off to sleep once more.


	10. Chapter 10

The Doctor lay feeling safe in his Alpha's arms. When he had first returned from the Master's room, he was confused and afraid. His body was begging him to run, but he couldn't. There was nowhere on the Valiant or in the entire universe that he could go, that the Master wouldn't find him. He didn't know what possessed him to untie Jack, but as much as he needed to run at that moment, he also needed his Alpha. Curling into Jack's arms had finally made him feel safe, but he still needed Jack to remove the feeling of the Master's touch and claim him as his own. He was upset when Jack at first refused to. Later when Jack agreed, he started to roll to his knees preparing to feel pain again. Jack had stopped him though and he was able to see the love in Jack's eyes as their bodies finally joined as one.

It still had hurt even though Jack tried to be gentle. He had clung to Jack, wanting Jack to stop while at the same time needing Jack to continue. Jack took his time, making sure that he found release from the act as well. Showing him that his body wasn't just a vessel for the Alpha to use but one that he could experience pleasure from as well. When Jack bit his shoulder in the same spot as the Master, he claimed him fully and the Doctor no longer thought of it as the Master's mark. After he laid his head on Jack's chest, listening to his heart. Though Jack was human, he would never leave him and the Doctor would never be alone again.

"Jack," The Doctor whispered, surprising Jack who thought he had fallen asleep again.

"Yes, sweetheart?" Jack wondered as he kissed the Doctor softly on top of the head.

"I didn't take the pill the Master gave to me," The Doctor admitted. He felt Jack tense for a moment before relaxing again.

"When should you have your heat again?" Jack wondered softly.

"I don't know. I have never had two heats consecutively," The Doctor responded. He turned his head so that he could look up at Jack. "I don't want to carry his child Jack."

"I will kill him before that happens," Jack growled angrily at the thought. No other Alpha was going to impregnant his Omega.

"You can't. In order for me to save the human race and the rest of the universe I need him to be alive. I am working on a way of stopping him, but it won't work yet," The Doctor informed Jack, choosing to remain vague in case the Master was listening. He hated the fact that it was going to be at least another seven months before he could stop the Master. He had to wait though, wait for the countdown to end so that hopefully the human race would gather together to stop the Master.

"How are you going to stop him?" Jack questioned him.

"Please just trust me, Jack," The Doctor begged. The Doctor sounded almost frantic as he squirmed against Jack. Jack pulled him up higher in his arms.

"I do trust you," Jack reassured him before biting down on the mark on the Doctor's shoulder. Jack had never wanted a submissive as his Omega, but if the Doctor needed to be dominated in order to feel safe, Jack could do that for him. He wrapped his arms around the Doctor holding him tightly to his body as he continued to bite the mark. The Doctor stopped squirming in his arms as he calmed down under Jack's reminder of his claim to his body. Releasing the Doctor's shoulder, he held him tightly still as he began to speak again.

"Doctor have you ever seen a broken Omega?" Jack wondered, his voice barely above a whisper. He didn't want Clive or anyone else to hear what he was about to ask the Doctor. He would have to find a way to make it up to Clive later but for now he had to make sure the Doctor was still near him when he went into heat again.

"Of course," The Doctor answered, looking up at Jack. The thought of being broken to the point where his mind wasn't even his own terrified him. Jack rolled the Doctor so that he could once more push into his body. The Doctor whimpered slightly as Jack moved above him. Jack leaned down and kissed the Doctor on the lips.

"Trust me," Jack whispered. He leaned down so that his mouth was right next to the Doctor's ear. He quickly whispered his plan in the Doctor's ear as he pushed slowly into his body. Leaning back he looked into the Doctor's eyes. The Doctor nodded slightly at him as Jack began to move. This time he was rough with the Doctor. Not to the point that he hurt him but so that the microphones would pick it up as the Doctor whimpered and cried out. He bit down hard on the Doctor's shoulder, lapping it with his tongue, before rolling off of him. Moving out of the tent, Clive stared at him.

"I did what you wanted," Jack growled at Clive. Clive looked over and could just see the Doctor's eyes peeking out of the tent. Upon seeing Clive, the Doctor moved further back into the tent and out of view once more.

"You were supposed to help him, not break him," Clive seethed at Jack.

"There was nothing to save," Jack hissed. He grabbed the bottle of water from the conference room table and took a drink of it. He offered some to Clive who glared at him. Shrugging he returned to the tent and closed it once more around them. "Come here," He barked at the Doctor. The Doctor moved quickly into his arms, laying his head on Jack's chest. Jack held him tightly as the Doctor looked up at him with trust in his eyes. Kissing him softly on the head, Jack closed his eyes too sleep.

-DW-

Jack was pleasantly surprised when the Master didn't return for the rest of the night. It allowed the Doctor to get the rest that he needed and began to heal his body from the trauma that it endured. Jack laid with him, not wanting to let the Doctor go as he protected him. As he climbed out of the tent, he didn't meet Clive's eyes. Instead, he headed to the table to eat. The Doctor peeked out of the tent but didn't move.

"Kneel," Jack ordered as he sat down at the table. The Doctor hurried across the floor remaining low to the ground. Reaching the table, he kneeled in the submissive position by Jack's legs. Jack grabbed a slice of bread off of the table and broke off a piece. He offered it to the Doctor, who took it gently with his teeth.

"You don't have to listen to him," Clive informed the Doctor. The Doctor looked over at Clive wearily. Jack growled and he quickly returned his eyes to the ground. Jack looked over at Clive who glared at him. Jack was now the second most hated person on this ship, but hopefully one day he could explain to Clive why. As long as the Doctor understood though, Jack would be able to get through this. He just had to continue to trust his Omega.


	11. Chapter 11

"Pretend to be broken." That was just part of what Jack whispered in his ear as their bodies joined together for a second time. Jack was rougher with him the second time, but he had to be. Jack was playing a dangerous game where he was making everyone on the ship think he was a dangerous Alpha. The Doctor knew better though and could see the love in Jack's eyes and the concern that he might actually be hurting him. Even Jack's bark of anger to join him to rest didn't really affect him. He still felt safe in his Alpha's arms and slept well without fear that the Master would come in and claim him back. Waking up that morning, he snuggled closer into Jack's arms. Jack kissed him softly on the top of the head and he turned to look up at Jack.

"Are you sure you want to do this," Jack hissed so softly the Doctor didn't hear him as much as read his lips. He nodded once more, showing Jack that he was willing to let Jack protect him. Jack kissed him on the head once more before moving out of his arms and leaving the tent. He watched Jack move across the room to the conference table with confidence. Clive glared at Jack the entire time but didn't look towards the tent.

"Kneel" Jack ordered as he sat down at the table. The Doctor hurried across the floor remaining low to the ground as the table, he quickly sat back on his heels as he dropped his head and clasped his arms behind his back. A moment later he saw a piece of bread being offered to him and he took it as gently as possible.

"You don't have to listen to him," Clive informed the Doctor. The Doctor looked over at Clive wearily. The other Alpha was angry, but the less people who knew the truth the better. Jack growled at him and he quickly returned his eyes to the ground. He took the next bite that was offered to him without complaint. He continued to eat until he heard the door to the room open. He trembled as he heard the familiar footsteps of the Master coming into the room.

Jack placed a hand over the mark on his shoulder. While it felt reassuring he also knew it was a way of showing his now claim to the Master. He heard the Master chuckle.

"You can't claim what is already mine," The Master informed Jack as he came closer.

"He broke him," Clive yelled from the corner. The Master abruptly stopped laughing.

"Theta come with me," The Master hissed. The Doctor whimpered but didn't move towards the Master. Instead, he lowered his head further and tried to make himself seem as small as possible. "What did you do to him?"

"I tried to claim back what was already mine. You had no right to touch him and if anyone is to blame for him being broken it is..." Jack's words were cut off by the sound of a gunshot filling the room. Jack's hand went limp on his shoulder. The Doctor jumped when the Master's hand touched his back. Feeling cowardly but playing his part, he quickly moved across the floor and back to his tent.

"Theta come to me. It's alright," The Master cooed at him. He peeked out of the tent as he looked at the Master crouching down in the middle of the conference room. He was looking at the Doctor with inquisitive eyes. The Doctor could tell that the Master was analyzing him for any signs that he wasn't really broken. He couldn't let the Master find them. He moved back further into the tent as the Master moved slowly closer. "I won't hurt you Theta."

"Doctor to me," Jack snapped right after he took his first breath of life. Barely thinking about it, the Doctor hurried out of the tent, around the Master and to Jack's feet. He knelt down in front of him, leaning into the comforting touch of his Alpha. The Master stood up straight and turned to look at Jack. The cold anger in his eyes was enough to make any man run, but Jack stayed where he was. He knew he was stronger than the other Alpha and if it came to another fight, he would win.

"Tish's arm is broke," The Master said as he walked over to Clive, ignoring Jack for a moment. You try to help her with her chores, I'll break her pretty little neck next. Is that understood?"

"Yes," Clive hissed.

"Guards," The Master called out. Three men rushed into the room. The Master pointed at Clive "Take that Alpha out of here and chain him somewhere that he can watch his daughter work." He waited until the four of them were gone before pulling his gun out once more. He didn't point it as Jack again though, but instead aimed it at the Doctor's head.

"You have one minute to get yourself to that corner and chained in or I will kill him," The Master informed Jack.

"You wouldn't," Jack growled at him.

"He is of no use to me broken. Fifty seconds," The Master answered as he released the safety on the gun. Jack stood and walked calmly to the corner. He chained his ankles into place, followed by his left wrist. The Master walked over and roughly chained his right wrist in place as well. Feeling movement, he looked down to see the Doctor pressing himself against Jack's legs. The Master looked at him with disgust before turning and leaving the conference room. Playing his part the Doctor curled up at Jack's feet and waited for his Alpha to be released.


	12. Chapter 12

Jack's arms were aching and his legs were numb by the time the Master returned. He jumped as the doors were flung open with enough force to slam them into the walls. The Doctor whimpered and scurried behind Jack's legs to hide as the Master entered with several guards. Two of the guards were dragging a man between them that Jack had never seen before. Not that he would recognize him anyway as the man's face was covered in black and blue bruises. He was bleeding profusely from his mouth and nose. The fact that his chest was still rising and falling amazed Jack, but he knew it was only a matter of time before the man succumbed to his injuries unless he had medical treatment. The fact that he was in this room meant that wasn't going to happen. He just hoped the man stayed unconscious until then so he didn't suffer anymore.

"I went to go and check the audio from last night and found several days have gone missing," The Master informed Jack as he stepped closer. Jack kept one eye on the Master but with the other he watched as the man was thrown to the ground in the middle of the room. "You wouldn't know anything about that now would you?"

"No," Jack answered him honestly. The Master stared at him for a moment and it felt as though the Master were staring into his soul.

"I thought not. Oh well, looks as though I am going to have to get my answers the hard way," The Master sighed. He snapped his fingers and two guards stepped forward. "Grab him."

"Leave him alone," Jack yelled as the guards moved not towards him but the Doctor. The Doctor cried out and tried to run from them. They easily caught him and hauled him off of his feet. Jack watched as the Doctor struggled.

"Jack," He screamed as he kicked at the guards. One got to close to his mouth with his arm and the Doctor bit down hard. The guard cried out, his grip slipping for a moment.

"Drop him and you won't live long enough to regret it," The Master hissed. The man tightened his grip, trying to ignore the pain in his arm as they moved towards the door. The Master turned to follow them.

"Where are you taking him?" Jack yelled. The Master ignored him as he turned off the light and left Jack alone in the dark. He wasn't alone long though before several men entered. Jack took a deep breath and prepared himself for the pain.

-DW-

The Doctor was almost in a full on panic as he was carried down the halls of the Valiant. He didn't know where they were going. The only thing he knew for sure was that if he ended up in the Master's room again, he wouldn't have to pretend to be broke anymore. They didn't turn towards the Master's room though. They continued down a long hallway to a room that had the door propped open. Inside the room, he saw medical equipment as well as a bed with restraints on it. He fought harder as he was laid down on the bed.

"Enough of this nonsense Theta," The Master hissed. He didn't listen though as he bucked and fought against the men. He managed to knock one of them down and tried to scramble away, just to be caught again. He felt one of the restraints clasp around his ankle and he screamed in frustration. By the time he was fully restrained to the bed he was a sweaty, shivering, squirming mess and several of the people in the room had bruises. The Doctor felt bad but not enough that he wouldn't fight them again.

"This will only sting a little," A young woman cooed as she came over with an empty needle. Another nurse joined her and held his arm so that he couldn't pull it away from them. He whimpered as she stuck it into the crook of his arm, drawing a full vial of blood. She started to remove the needle, but the Master stopped her.

"Draw another," The Master told her.

"Yes sir," She answered without hesitation. She removed the empty vial and put a fresh one on filling it as well before finally removing the needle.

"You brought this on yourself Theta," The Master growled as the nurses left the room with his blood. "Hiding your Omega scent all these years from me. If you would have just submitted to me, you could be laying in my bed your stomach full with my child, rather then strapped to this bed." The Doctor stared vacantly at him as he continued to shiver and squirm against the restraints.

"You also leave me with a problem Theta. I want to know what happened in that room, but I can't look into your mind without destroying it if you really are broken." The Master paused as he looked at him questioningly. "Oh well, my men will torture it out of Jack soon enough."

"Jack," The Doctor whimpered as he looked around the room anxiously. The Master covered him with a blanket and then left him alone in the bed. The Doctor continued to squirm and fight. It was wearing him out, but he couldn't drop the act even for a moment. Eventually though his body couldn't take it anymore and he dropped off to sleep. He woke with a start as footsteps approached the bed he was laying on. He once more began to fight against the restraints and to get away from the people surrounding him.

"You lied to me Theta," The Master whispered. The Doctor looked up at him with wide frightened eyes. "You didn't take the pill I had the guards give you. Don't worry they will be punished for the mistake. Now take your medicine like a good boy." The Master grabbed his head and held it still as one of the nurses tried to put the pill in his mouth. He sucked in his lips and held them closed tightly, not allowing her to.

"Just open up," The nurse told him. He whimpered as he sucked his lips in further to keep her from giving him the pill. He breathed a sigh of relief when the Master released his head. His relief didn't last long though as the blanket was pulled down and his ankles were unhooked from the bed. He barely had time to react as the Master grabbed his legs and forced them into the air, exposing his bottom. He cried out as a finger was pushed roughly into his body by one of the nurses.

"Next time you will take the pill without fighting me," The Master told him as he continue to hold his legs. The nurse pushed the pill deeper as he squirmed against her before finally moving away. He fought as the Master rehooked his legs to the bed, but it was halfheartedly. He felt tears wailing up in his eyes and he didn't try to stop them. He wanted to be back in Jack's embrace even more then he wanted the TARDIS back at the moment. The Master brushed his hair away from his forehead and he didn't fight him. He just laid there limp on the bed staring at the ceiling. Seven more months he reminded himself, and then this hell would be over. At that moment though, seven months seemed like an eternity.


	13. Chapter 13

The Doctor wasn't left alone for the next few hours as he was examined head to toe by the nurses. They checked, his temperature, his hearts and his lungs as well as took CT scans and x-rays. The Doctor fought them at first. That was until the restraints were tightened to the point they had absolutely no give. He lay their wide-eyed and terrified, shaking his head at them. It did him no good though as they continued to examine him. He reached his limit of the feeling of their hands as they examined his genitals. It was then that he began to shut down. He closed his eyes and trembled trying to keep his mind from slipping and then he was alone.

He didn't know how much time passed as he laid strapped helpless to the bed. Occasionally the door would open and someone would come in. They would take vitals, draw blood or offer him something to eat and drink. The Master was never with them and he couldn't help but wonder where the Master had disappeared to as he was left alone with his thoughts. It was during the time that he was restrained that he figured out that the Toclafane where the same humans he met that were looking for Utopia. That thought alone was enough to make him want to give up. The fact that the humans he loved so much were part of the hell the Master was bringing to the universe.

He slept more than he ever had before because there was nothing else to do. Time had no meaning to him anymore. He knew he should be worried about the countdown and stopping the Master, but even that seemed beyond his control at the moment. Nothing his was his own anymore except for his mind and even that was slipping away from him. Not that he cared. He stopped eating, stopped drinking, stopped living really as he let himself waste away on the bed. Eventually, he heard the door open and close, then open again.

"You have five minutes with your Omega," The Master hissed before the door closed again. He heard footsteps approaching the bed. The bed dipped as someone sat down on it. He opened his eyes as he felt a gentle caress across his head. The sight didn't make him feel any better. Jack looked like he had been in a fight. His body was covered with bruises and he was bleeding from several cuts.

"You're alright," Jack cooed softly. The Doctor turned his head to expose his neck and Jack leaned down, biting softly on his claiming mark. The Doctor could feel that Jack had several missing teeth but still the reminder that he was Jack's Omega comforted him. For the first time in days he remembered that he couldn't move. He tugged weakly against the restraints, wishing he could hold Jack. Jack wrapped him in a hug, kissing him softly on the cheek.

"I want to go back to the tent," The Doctor whimpered.

"I know, but you just have to stay here a little while longer," Jack lied. In reality, he didn't know how much longer the Doctor was going to be kept away from him. His own life had become a never-ending onslaught of beatings and torture, as they tried to find out what the Doctor and him spoke about. He lied of course, letting little bits of information loose to make it look like an accident. As far as the Master was aware, the Doctor and Jack were planning on running away together. The man who was killed had been aware of their plans, but he had agreed to erase the tapes if he could go with them. It was all an elaborate lie that took a lot of effort to remember as he was hit. Jack sat up so that he could look the Doctor in the eyes. "I had no choice but to tell him what we talked about. I tried to resist, but he forced it out of me."

"I forgive you Alpha," The Doctor whispered. He smiled as Jack leaned down so that he could cup Jack's face in his hand. He tenderly ran his hand over Jack's cheek. Jack winced as the Doctor touched the swollen muscles, but he didn't pull away. Jack turned his head, so that he could kiss the Doctor's palm.

"The Master tells me that you have stopped eating. You need to eat and drink sweetheart," Jack told him. That message was the main reason he had been allowed in the room. The Master wasn't going to let the Doctor just die and Jack was the only one who could get him to eat. As the Doctor's Alpha he could order it and if the Doctor was truly broke, he would listen.

"I will," The Doctor agreed. Seeing he had no other choice.

"No matter what happens, never forget that I love you," Jack said softly as he kissed the Doctor's palm once more.

"Jack, take me with you," The Doctor begged. He didn't like the fact that he was begging. It wasn't just an act that he was putting on for the Master. He really needed to be with his Alpha and being separated from him, was tearing him apart inside.

"I can't. Just be strong a little longer. Promise me that you will be strong." Jack moved his head up so that he could nip the Doctor's neck once more. The Doctor groaned as Jack released his neck and kissed him on the cheek.

"I will," The Doctor promised. Jack stood up as the door opened once more. The Doctor didn't want Jack to go, but he could see that Jack didn't have a choice. Outside the door, more than a dozen guards were waiting for him and if Jack refused to leave willingly he was to be drug out. He moved towards the door, keeping his head held high. He wouldn't let the Doctor see any more of the pain the lie was causing him. He would keep the Doctor safe even if it meant he lost his own sanity in the process.


	14. Chapter 14

Jack was taken down to a small room in the middle of the ship. Everything in him told him it was a bad idea to enter the room. The room is where he had been hung by his wrist and tortured by the Master.

"Go or I kill him," The Master hissed. Jack held his head high as he entered the room and walked over to the chains. They were covered with dry blood, but the Master didn't bother to have them cleaned before securing them once more around Jack's wrist. He didn't see a point as the blood was Jack's anyways. Once the chains were secure, Jack was hoisted into the air by his arms until just the tips of his toes could touch the floor.

"What do you want now?" Jack wondered trying to sound bored and not let his fear show through.

"I want you to order the Doctor to my bed," The Master told Jack. Jack couldn't help the chuckle that escaped and he was rewarded for it by a fist to the stomach. "One way or the other, I am going to claim and breed your precious Omega. You can either order him to my bed or I will take him by force."

"He will never submit to you," Jack hissed. The Master moved closer to Jack, running a hand down his cheek.

"You act like he will have a choice. Soon the whole universe will submit to me and your precious Doctor will carry my children like a good Omega," The Master informed Jack.

"Over my dead body," Jack laughed.

"That can be arranged," The Master answered. Jack rolled his eyes at the Master as the barrel of a gun was pressed to his forehead. They both knew it wouldn't keep him dead for long. "Or I can just kill Theta."

"You wouldn't. You need him," Jack yelled, all the humor gone.

"If he refuses to carry my children then he is no use to me. Think about it," The Master replied as he pulled the trigger. Jack's body went limp in the chains as his head fell forward "Or don't."

-DW-

When the door opened again, the Master came into the room alone. He closed the door behind him, making sure to lock it before coming over to the bed. The Doctor stared at him wide-eyed, knowing that something was going to happen that he didn't like. Sure enough, the Master unhooked his left leg from the bed before climbing up onto it. He held his leg as he unstrapped the right one as well.

"Don't," The Doctor whimpered as both his legs were lifted in the air and the Master settled between them.

"Ever since learning that your mind was broke I have considered just killing you," The Master informed him. He watched helplessly as the Master pulled his zipper down and moved closer. "I have had my people run extensive test on you though, and they have agreed that while your mind is broke you will still be able to carry my child."

"Jack's my alpha," The Doctor informed the Master. His voice was so low that he doubted that the Master heard him. He tried not to scream as the Master forced himself into his body. He curled his hands into fist and stared at the ceiling as the Master began to move.

"I am your Master and ruler of Earth. There is no one above me period. Your body is mine to claim and breed as I see fit," The Master informed him, his movements going rough for a moment before returning to an easier to handle pace. "The sooner you accept me as your Alpha the easier this will be on you."

"Never," The Doctor hissed. He recieved a slap across the face for his arguing. He wanted to glare at the Master, but a broken Omega wouldn't dare look an Alpha in the eye. Especially one who was claiming his body. Frustrated, he first looked down where he was joined with the Master. Feeling ill from the sight, he turned his head to look at the wall.

"You will help me to rebuild the Time Lord race, regardless of whether or not you agree. I am going to keep you full of my children and you will give birth to strong Alphas or I will punish you," The Master informed him. The Doctor huffed. He had no choice over the gender of the child, let alone what they would present as. He didn't plan on being with the Master that long though. This ended with the countdown. He just had to make sure the Master didn't kill him before then. He groaned as he felt the Master find his release deep inside his body. The Master moved off of him, tucking himself back into his trousers. He went to the door and left, leaving the Doctor chained to the bed, his legs splayed at an odd angle as he tried to keep pressure off his bottom.

A nurse rushed in a moment later. She cleaned him up and tucked him back into his blanket. Try as she might though, she couldn't coax him to take a bite of food. The Doctor felt sick at the sight and smell of it as he thought about carrying the Master's child. His body wasn't the Master's to claim. Jack was his Alpha and he would happily care Jack's child if he had too. His body wouldn't be able to successfully carry the child if he didn't receive the nutrition he needed. His mind made up he refused the meal and if the Master continued to claim his body, he didn't know if he would ever eat again.


	15. Chapter 15

"What are you planning?" Jack wondered as he laid down on top of the Doctor inside his tent.

"I can't tell you," The Doctor answered him just as softly. He trusted Jack, but if the Master knew that Jack knew his plan, he would stop at nothing to get the information out of Jack.

"But you still need time," Jack questioned as he spread the Doctor's legs apart. The Doctor nodded. "I can give you time, but you have to pretend to be broken. It won't stop him from claiming you, but it will give you a chance to heal," Jack had whispered desperately as he pushed into the Doctor's body for a second time as his own.

"How?" The Doctor wondered as Jack nipped at his ear.

"Broken, you will no longer seem like a threat. Think about it," Jack hissed. Jack leaned back to look in his eyes and he nodded. The choice was his, and Jack was given him an opportunity to make the Master ignore him. It had been hard to think as Jack took his body roughly, but it was even harder to remember why he had agreed as the Master did the same. The Doctor though just found himself waiting impatiently for the Master to finish. As soon as the Master did, the routine had been the same for the last few days. First, the Master would leave and a nurse would come in and clean him up then try to get him to eat. He would also get a nice hot cup of tea. Then he would be ignored for hours on end until they tested him again or until someone remembered he was in the room. The Master though had other ideas. As soon as he finished, he stood up and went around the bed unhooking the Doctor's arms.

"You are to follow me. If you even think about wandering off, there are guards who won't hesitate to drag you to another room and beat you within an inch of your life," The Master threatened. The Doctor rolled off the bed, immediately collapsing onto the floor as his unused muscles had trouble bearing his weight. "Get up," The Master hissed. He tried to stand, but he couldn't. The Master kicked him hard in his side. "I said get up."

"I'm trying," The Doctor argued. He wondered how long he had been chained to the bed that atrophy was setting in.

"Try harder," The Master seethed. He kicked the Doctor again. The Doctor thought for less than a minute what a broken Omega would do before he latched onto the Master's leg with his teeth. The Master howled in pain, slapping him hard across the head. He released his grip, falling back. "You'll pay for that."

"Are you alright sir," A guard asked from outside the door. The Master limped over to the door and opened it.

"Grab him and follow me," The Master ordered. The guards grabbed his arms tightly and drug him down the hall after the Master. The Doctor wasn't surprised when they ended up in the conference room. In the corner of the room, Jack was hanging by the chains again. Though he was dirty, he had obviously died recently as his body showed to marks from the torture he received. The Doctor smiled weakly at him before looking towards the table. Around the table sat several men and women that he didn't recognize. The Master sat down at the head of the table and he was dropped unceremoniously by his feet. He yelped in pain before scrambling as quickly as he could into the submissive pose. The Master glared at him as he began to speak to the people gathered around the table.

The Doctor should have listened to them, as it could have been information that he needed. He heard mention of the rockets and glanced up at the clock on the wall. The countdown showed that he had little more than six months left before he would be free of this nightmare. He didn't care as he turned his attention back to the floor, letting his eyes drift closed. He was rudely awoken by a kick to his side. He glared at the owner of the foot for a moment.

"Remember your place Theta," The Master hissed. Rolling his eyes, he turned his attention back to the floor. He was going to pay for his transgressions and he knew it. Sure enough after the meeting was over, he was hauled to his feet and bent over the table. Two guards held his arms keeping him in place as the Master stood behind him.

"I never gave you permission to touch him," Jack yelled from the corner.

"Yet I have anyways," The Master responded. Though the Doctor couldn't see the Master's face he could hear the smile that Master had.

"I am going to kill you," Jack hissed.

"And I am going to punish Theta for that remark as well as his own," The Master replied. The Doctor felt the first slap against his backside. He cried out in surprise but then managed to bite his tongue to stop from responding again for a while. The slaps just kept coming though and soon the tears were flowing freely down his face as he tried to move away from the Master's hand. His bottom burned and he whimpered and squirmed trying to get away from the guards. He thought his punishment was over when the Master stepped back, but another man took his place.

"Leave him alone," Jack screamed at them. He had been yelling at them since the punishment started but had been ignored as he was forced to watch. From his viewpoint, he could see the Doctor's bottom was a bright red. Ever slap darkened the skin as the Doctor's hands curled tightly into fist. As the punishment continued, he turned his head to the side and had it resting on the table. Jack could just see the tears flowing freely down his face. Finally, the second man stepped back and the guards released his arms. He fell to the floor curling up in a ball. The Master stepped over him and grabbed the Doctor's sweat drenched hair.

"Next time you will listen to me," The Master hissed. Releasing his head, he left the room, taking the guards with him.

"Are you alright sweetheart?" Jack questioned as the Doctor didn't move. Hearing his voice, the Doctor lifted his head slightly. His body hurt and he couldn't put any pressure on his bottom. He wanted to go to Jack but he couldn't find the will power to move. Instead, he curled into himself and shivered on the cold conference room floor.


	16. Chapter 16

Jack felt completely helpless as he stared at the Doctor from the corner. The chains prevented him from going over and checking on his Omega and if he had ever felt more worried about the Doctor he wasn't sure. The Doctor had stopped shivering about an hour ago. Now he just laid in the same spot that the Master had left him in after his brutal spanking. He didn't move, didn't speak and Jack couldn't tell whether or not he was breathing as he remained half curled up on his side. He didn't think the Master would intentionally kill the Doctor, despite his threats, but accidents did happen.

"I know you are hurting and cold Doctor. Why don't you come over and lean against my legs for warmth," Jack suggested to the unmoving man. "Or there is a bottle of water on the table. You could have a nice drink of it." There remained no reply from the Doctor.

You're really starting to scare me," Jack informed him. Jack looked up at the shackles that held his wrist in place. It had been awhile since he actually tried to figure out if he could get free. Now he tested the give on them. If he pulled hard enough he might be able to pull the shackle out of the wall. It was a long shot and would make a lot of noise if he succeeded. For now it was best to just continue talking to the Doctor and hoping he would get an answer.

"Sweetheart I really wish you would move or do something that showed me you were alive," Jack told him softly. The Doctor didn't move still. Jack watched on continuing to talk softly to the Doctor. It wasn't the Doctor who reacted though. Jack jumped slightly when he heard the door to the conference room being opened. The Master had been listening in and was curious about the Doctor as well. He still fully planned on breeding the Doctor and he couldn't do that if the Doctor was dead. He walked over to the Doctor and knelt down beside him. The Doctor looked up at him before returning his attention to the leg of the table.

"He is alive," The Master informed Jack as he stood up. "Now quit your whining or I will have you removed from this room."

"He is obviously in shock. Let me tend to him if you plan on keeping him alive," Jack snipped. The Master stared at him as he considered it.

"I have nurses to take care of him," The Master informed Jack.

"Then take him to them and let them tend him, but help him for god's sake," Jack yelled. The Master walked over to the door. As he approached it he motioned to his guards. Jack was slightly surprised when they didn't go to the Doctor but instead came over to him. He tensed as he waited for the first blow to fall and to be punished for yelling at the Master. Instead, he felt the shackles loosened from around his wrist. He contemplated for a half a second about going and killing the Master first before he rushed to the Doctor's side.

"I'm here," Jack whispered as he dropped to his knees beside the Doctor. Being careful of the Doctor's bright red bottom, he scooped him up into his arms. The Doctor wrapped his arms around Jack's neck to hold on, but other than that didn't react at the change in position. Jack carried him over to the tent, laying him down on the thin blanket. He wrapped the blanket up around the Doctor, trying to warm up the cool body. He knew the Doctor's natural body temperature was cooler than a human, but he felt too cold for Jack's comfort. He wanted to lay with him to warm him up. He needed to grab a few things though. Standing up straight, he first returned to the table to grab the bottle of water. Next he looked for anything that the Doctor could eat, finding nothing he returned to the Doctor. He sat the bottle of water just outside of the tent before laying down behind him. Carefully pulling the Doctor into his arms to warm him up, he grabbed the bottle of water. He helped the Doctor to take several mouthfuls before setting it aside again.

"I've missed you," The Doctor whispered after a few minutes. He turned his head slightly to the side and Jack bit down on the claiming mark. He moved back slightly so he was pressing closer to Jack. His bottom stung as it pressed against Jack's body, but he tried to ignore the pain. He wanted to be as close to Jack as possible. Reaching back, he moved the blanket out of the way and pressed himself further against Jack. Jack released the bite on his shoulder for a moment.

"Maybe we should wait," Jack hesitated not wanting to hurt the Doctor more.

"Please Jack," the Doctor begged. Jack could never resist the want in the Doctor's voice. As gently as he could, he pushed himself into the wanting body. The Doctor groaned loudly as Jack body smacked against his sore bottom. It hurt but at the same time it was Jack claiming him and it felt right. Not like when the Master took advantage of the fact he was tied helpless to a bed. Jack nipped his shoulder again as he made sure the Doctor found his release first before following him over the edge. After he pulled the blanket over the both of them, cuddling the Doctor close.

"Jack," the Doctor spoke up as he continued to lay in Jack's arms.

"Yes sweetheart," Jack wondered.

"You're not going to leave me once this is over, are you?" The Doctor questioned. He turned his head so that he could look at Jack. Jack leaned over and kissed him softly on the lips.

"No, I am going to be by your side as long as you will have me," Jack promised. He settled back down pulling the Doctor closer to him. "Rest now."

"I'm not tired," The Doctor yawned and Jack chuckled. He kissed the Doctor on the back of the head and then bit down gently on his shoulder once more as he tightened his grip. Safe in his Alpha's embrace the Doctor was soon fast asleep.


	17. Chapter 17

Jack didn't mean to fall asleep as he lay holding the Doctor. As he woke up he noticed a familiar scent. Without opening his eyes, he took a deeper breath. The smell went straight to his groin as he realized that the Doctor was approaching his heat. Jack tried to remember if the Doctor had the scent yesterday, but then he had been too worried about his Omega to take notice. Jack didn't know if the Doctor was in heat because it was actually his time again or if being with his Alpha had sped up his body's response. The Doctor's heat could have also been sped up by the fact that his body was being claimed repeatedly. Regardless of the reason why he was going into heat, the one thing on Jack's mind was that he had to claim the Doctor before the Master noticed. Being as gentle as possible, he rolled the sleeping man on to his back. Settling between the Doctor's legs, he pushed them into the air as he eased himself into the Time Lord's body.

"Jack," The Doctor cried out as he jolted awake. He scrambled to grab onto something, clawing at Jack's back in the process.

"I'm sorry," Jack whispered as he leaned down so that his head was nestled in the crook of the Doctor's neck. "I'm sorry. You... and I can't..."

"It's alright Alpha," The Doctor informed him as he felt the hormones racing through his body. Jack joining with him was bringing his heat on faster and stronger than ever before. His body craved the Alpha's touch and he couldn't be mad at Jack for wanting to claim him. One way or another he was going to be pregnant before this year was up. He just wanted it to be Jack's child that he was carrying and not the Masters. Jack bit down on his shoulder as he found his release for the first time. He didn't let the Doctor go though as he continued to hold him.

"Need you," Jack moaned as he started to move again. It was during the fourth time that Jack claimed him that the door to the conference room opened. Even in his heat, the Doctor was mortified to have the Master find him laying on his back with his legs in the air. Jack was still moving between them and he growled as the Master came towards the tent.

"You lied to me about him being ill," The Master hissed as he saw them. One breath was all it took to smell the heat pheromones in the air. The Doctor tried to hide his face in the blanket, but Jack wouldn't let him. Jack stood up and moved between the Doctor and the Master.

"He is mine," Jack growled back. He moved towards the Master ready to fight him. The Master though knew he would lose in a fair fight. So rather then fighting fair, he pulled out his gun and shot Jack clean between the eyes. Jack fell to the floor midstride.

"Guards," The Master called out. Two guards rushed in. "Take him and chain him down in the engine room."

"Yes sir," The guards answered. They grabbed Jack's arms and hauled him out of the room as the Doctor watched on. He didn't have time to wonder if he would ever see Jack again as he was rolled onto his hands and knees. The Master quickly pushed into him from behind taking him roughly.

"You will never see Jack again," The Master informed him. "I am your Alpha now and the sooner you realize that the easier this will be on you."

"Yes Alpha," The Doctor moaned. He gripped his thin blanket in his hand as he bit down on it.

"Oh and you better hope you aren't carrying that thing's child or I will kill the both of you," The Master hissed in his ear. The Doctor didn't reply. It would take at least a month or two before they knew he was pregnant. The Doctor had no doubt that it would happen, but it would be after he gave birth before the Master could determine whether or not it was his or Jack's child. By then time would hopefully be reversed and he could pretend he was the strong beta again not the broken Omega that he had been forced to become.

-DW-

As the next two months passed. The Doctor didn't see or hear about Jack. Life aboard the Valiant though had almost become tolerable as he was forced to stay in the conference room. He was given his clothes back as the Master wanted no one else to see his naked body and he was given a wheelchair that he was forced to use. His only company was the Master and a few nurses who came into the room regularly to check on him and feed him. Though the food was still scarcer than he would have like, he was given vitamins as well to try to keep him healthy. He quickly learned to take the pill or he was given an injection of the pill instead. He hated the injections as they always hurt as a punishment for him not taking the pill.

During the two months, no one had been allowed to touch him except for the nurses and the Master. He was still punished for not listening, but the beatings were kept to his legs and his feet. Though he hated the wheelchair, he was also slightly thankful for it as he his legs were often so black and blue that it hurt to walk.

This morning he wasn't alone in the conference room as the Master had brought in the leaders of the new countries. With nothing else to do and because he was not seen as a threat, the Doctor listened into the meetings. Mostly they were about the progress of the rockets that were being built and about rebellions that had been squashed. Today though the Doctor perked up a little as for the first time in a few months he heard conformation that his plan might still work.

"We have heard rumors that Martha is heading across what was once Jordan," One of the men stated.

"She was killed in Japan," Another one argued.

"They never found her body and there was no confirmation of her death," The first man stated. He turned to look at the Master. "I have sent my men to investigate and if she is found, she will be killed."

"No," The Master said. "I want to be the one to kill her. If she is found, I am to be contacted at once. Is that understood?"

"Yes sir," The man answered. The Doctor smiled as he hung his head. Martha was alive and in four months time she should be back in England. He heard the meeting being dismissed and the Master came over to him. He quickly wiped the smile off of his face as he looked up at his fake Alpha. No matter what the Master said he would never accept the Master's claim over his body.

"I saw that smile Theta. Regardless of whether or not your little pet is alive now, I will soon kill her. Now you are lucky I don't have time now to punish you. The nurses are waiting to test and find out whether or not I have successful bred you," The Master hissed at him. He put a hand on his stomach as he was pushed out of the conference room and towards the infirmary.


	18. Chapter 18

The Doctor climbed up onto the bed as the Master set up the equipment. He was a little slow as his legs ached painfully with every movement. The Master didn't try to help him, but instead stood there staring at the Doctor impatiently.

"Move faster Theta," The Master hissed at him.

"I'm trying," The Doctor replied. His legs barely wanted to support his weight and it took all of his strength to climb up on the bed. Once on it, the Master lifted his shirt up. The Doctor hissed as cold gel was squirted onto his stomach and the Master pressed the wand against it. It didn't take long for the Master to find the tiny fetus nestled within his abdomen. The Doctor stared at the picture on the screen as he silently hoped it was Jack's baby.

"You're lucky it has two hearts or I would be terminating the pregnancy. As it is you better hope the blood test come back that it is mine once it is born," The Master stated. He didn't let the Doctor look at the screen any longer as he moved the machine away from him. Standing up he grabbed an empty syringe. Finding a vein he stabbed the needle into the Doctor's arm, making him cry out in pain. He filled the syringe to the top and then pulled it out. He didn't bother to place a plaster over the site as he capped the needle and set it aside. "Take your trousers off."

"Why?" The Doctor questioned as the Master removed his own belt. He didn't move to follow the Master instructions and the Master narrowed his eyes at him.

"That is now three. I suggest you remove your trousers quickly before I add a fourth one to the total," The Master sneered. The Doctor quickly unbuttoned and started to pull down his trousers. The Master grew impatient with him though and grabbing his trousers at his ankles pulled them off his legs. The Doctor watched fearfully as the Master dropped the trousers on the floor and then hit his belt against his hand. "You will receive ten slaps for each transgression and you will count them."

"Thirty sir," The Doctor answered him with a moan.

"Oh I think not. I counted four transgressions not three. That will be forty slaps. Now count," The Master stated as he aimed the first blow onto the Doctor's thigh. The Doctor cried out and almost missed the first count.

"One sir," He counted, his voice shaking. By the time the Master finished his punishment, he was sobbing so hard that he could barely count. He had counted all forty of them but had received ten more for not thanking the Master for punishing him. The Master picked his trousers up off of the floor and threw them at him.

"Clean yourself up and get dressed quickly. I expect you in the conference room in no more than ten minutes," The Master hissed. He turned and walked out of the room. The Doctor trembled slightly as he tried to move and get dressed. Thankfully one of the nurses took pity on him. She wiped down his legs with a clean cloth, helped him to dress and then assisted him into the wheelchair. By the time he made it to the conference room though he had just seconds to spare. The Master looked up at him and didn't say a word as he grabbed the wheelchair and pushed him so that the wheelchair hit the wall jarring his body. The lights were turned off and he was left alone in the room with his thoughts.

"Please don't be the Master's child," He whispered to his stomach as he placed a protective hand on it.

-DW-

Four Months later

The Doctor was sitting on the floor inside his tent. He was six months pregnant now with his daughter and his stomach clearly showed it. The Master had made sure to find out the gender as soon as he could. The Doctor had been beaten again when the test had revealed he was having a girl rather than the boy that the Master wanted. The Doctor was happy with the fact that he was having a little girl though. He had always wanted a daughter. He looked up as the Master let out a whoop of joy. If the Master was happy that meant something was about to happen that he didn't like.

"Theta come out here," The Master called out happily. The Doctor carefully got out of the tent and into his wheelchair. "Now don't look so gloomy Doctor. In a little more than an hour, the rockets are going to launch and to top it all of Martha has been found. So I also get the satisfaction of killing her."

"You don't have to," The Doctor told the Master. The Master looked at him sympathetically even though he still had glee in his eyes.

"Oh but I do, thanks to you Doctor. Sending her out to assemble a gun to kill me. That was very naughty of you. Lucky for you, I am a forgiving man and I won't punish you for it," The Master lied. The Doctor huffed. He had already been punished for it, time and time again. Still with the countdown ending soon that meant he would finally be free of his torment. He only had one chance to end this, if he messed up, he would be in the Master's grasp forever. He checked again to make sure that he was linked properly with the network.

The Master disappeared from the room. The Doctor was left alone again until the door opened once more. He looked up expecting to see the Master was returning. Instead, he was surprised to see the Jones family being led in. Francine was thinner than the last time he saw her and Clive's eyes were haunted. Tish's arm was bent at a strange angle and she held it away from her body. He couldn't help the smile that crossed his face though as Jack was led in behind the rest. He was covered in dirt and his clothes were torn and ragged. His eyes were bright though and he smiled back upon seeing the Doctor. He was taken to the other side of the room away from the rest.

The Master entered a moment later. The grin on his face was large and the Doctor expected to hear that Martha was dead. She entered the room though shortly after with more guards flanking her. He winked at her and she winked back. Looking at the countdown he saw he had less than five minutes left. Soon they would be free.


	19. Chapter 19

"Citizens of Earth, rejoice and observe," The Master announced happily as Martha approached him. Martha held her head high. In her eyes there was no fear but a coldness that she didn't have before. The year walking the Earth had changed her and the Doctor wished that it had gone differently. That she would forget what happened to her and the youthfulness would return to her eyes. She was in the eye of the storm now and the Doctor knew she would never be the same. She stopped in front of the Master staring him straight in the eyes.

"Your teleport device, in case you thought I'd forgotten." The Master held out his hand for it. Martha didn't look down as she took the device off of her wrist. Rather than handing it to the Master she threw it to the side. The Master's eyes narrowed as it hit the wall. He didn't retrieve it though.

"Kneel."

"No," Martha replied standing her ground. The Master pulled his gun out and pointed it at Tish.

"I said kneel," He hissed. Martha got slowly down on her knees, keeping her eyes on the Master. Happy that she listened he turned to the small screen next to him and pressed a button. The screen came on with one of the men the Doctor had seen in the meeting. He turned his attention briefly from the screen to look at the timer. Three minutes remained until the launch. The Doctor realized that the Master was still talking and turned to look at him once more. "At zero, to mark this day, the child Martha Jones, will die. My first blood. Any last words?"

"Go to hell," Martha responded.

"Such a disappointment, this one. Days of old, Doctor, you had companions who were worth something. This one's useless. Bow your head," The Master demanded. Martha continued to stare him straight in the eyes as he pointed the gun at her. She couldn't help the smile that crossed her face and she chuckled. The Master narrowed his eyes further. "What's so funny?"

"A gun," Martha snickered. "A gun in four parts."

"Yes, and I destroyed it," The Master answered annoyed with her.

"A gun in four parts scattered across the world? I mean, come on, did you really believe that?" Martha asked him snidely.

"What do you mean?" The Master sighed.

"Like I would ask her to kill. You always have missed the obvious," The Doctor told him.

"Omegas do not speak," The Master snipped at him.

"Only if they truly believe they are Omegas," The Doctor replied. Out of the corner of his eye, he could see Clive staring at him opened mouthed. For months now he had believed Jack broke the Doctor and now here he was arguing with an Alpha. The Master walked over to the Doctor. Reaching down he grabbed the Doctor's thigh in his hand making the Doctor cry out in pain.

"It doesn't matter. I've got her exactly where I want her," He hissed at the Doctor. Releasing his grip he turned back to Martha as she started to speak again.

"But I knew what Professor Docherty would do. The Resistance knew about her son. I told her about the gun, so she'd get me here at the right time," Martha informed the Master.

"You're still going to die," The Master told her as he moved back to stand in front of her. He aimed the gun once more at her, but she didn't flinch. She had faced nightmares that she had never dreamed of during this last year. The Master killing her would be a relief in some ways. She wanted to live for her family but if she died now on the Valiant at least she would die with the knowledge that she helped to save them.

"Don't you want to know what I was doing, travelling the world?" She didn't give the Master a chance to answer her as she continued. She told him about traveling and telling everybody about the Doctor. The Doctor had always left before people were able to learn his name. Just this once though, everyone in the world knew he had saved them time and time again. They knew he would be there whenever he could and that if they thought of him with the countdown he could save them all.

As the countdown reached zero, the Doctor felt the network responding to him. He had plenty of time to think about what would happen when he connected to the network. In his dreams, he saw himself healing fully as he floated towards the Master on a field of energy. With one flick of his hand, the Master's laser screwdriver would go flying across the room and the Doctor would forgive him. Reality was nothing like his dreams though. From his wheelchair, he broke the connection with the network. Awareness showed in the eyes of the guards on board as they saw the Master for who he really was and not Harold Saxon as he claimed to be.

"I've had a whole year to tune myself into the psychic network and integrate with its matrices," The Doctor informed the Master as he pushed himself painfully to his feet. "The one thing you couldn't do is stopping them from thinking."

"I order you to stop this nonsense," The Master hissed. The Doctor didn't listen as he took a small step forward, followed by another. Every step felt as if he were walking on broken glass and his legs burned with the effort. The Master pointed his laser screwdriver at him as he hobbled closer. He bit back the cry of pain as the screwdriver cut his arm.

"Doctor," Jack cried out with worry. The Doctor held up his hand to stop him from rushing forward.

"It's over now. We have control of the Valiant. Give up and come with me back to the TARDIS," The Doctor told him.

"So you can keep me as your prisoner?" The Master questioned. The Doctor nodded.

"If I have to," The Doctor replied moving closer. The Master pulled his gun out and pointed it at him.

"Put the gun down," A guard order. Rather then listen the Master released the safety. The Doctor froze as the sound of a gunshot filled the room. He quickly assessed himself but realized that he wasn't hit. Instead, the Master was sitting there looking stunned as blood seeped from his abdomen. As carefully as he could he dropped to his knees beside the Master.

"It's just a little bullet wound. Regenerate," The Doctor told him.

"No," The Master replied. The Doctor felt a hand on his shoulder and he looked over as Jack knelt down next to him. The Doctor refused to beg the Master to regenerate. He had played the part of a broken Omega long enough. He may have been born an Omega but he was a Time Lord and an Alpha. He sat a little taller.

"The Paradox Machine still needs to be destroyed," The Doctor informed Jack.

"Will you be alright," Jack wondered.

"Fine," The Doctor answered. Jack kissed him on the head before motioning to the guards to follow him. As they disappeared the Doctor turned to look at the Master once more. The Master was struggling to breath now. Reaching out the Doctor took his hand gently in his own as he the Master took his last breath before going still on the Valiant floor. Not even a minute later the room began to spin as time reversed itself. For the people of Earth the year never happened. The president and the Master were both still dead but the millions who had been killed would once again live. The Doctor didn't know how long he sat there staring at the Master's body before he felt gentle hands on his back.

"Come on Doctor. Let's get you off this floor," Jack whispered.

"I can't walk far," The Doctor answered him softly. The shock of his childhood friend dying hadn't worn off yet. Once it did Jack knew the Doctor would break down. They both had experienced hell during the year at the hands of the Master but that didn't change the fact that the Doctor had once cared for the man. Jack tried to be gentle as he picked up his Omega but the Doctor still cried out and writhed in pain as he was carried back to his wheelchair. Jack carefully sat him in it.

"You're an Omega," Martha asked confused. The Doctor looked over to see her huddled with her family. He put a hand on his stomach as he nodded.

"I'll explain everything later," The Doctor told her. "I can even give you a lift home in the TARDIS. It is going to be a few days though as we have to remove the paradox machine."

"Thank you, but we have already been offered a ride home," Martha replied. She came over and wrapped her arms around him in a tight hug. "I will be seeing you again soon though." He hugged her back and then watched her leave with her family. Wheeling himself towards the door, he headed towards his TARDIS. She had a lot of work that needed to be done before he could try to get his life back.


	20. Chapter 20

Jack followed the Doctor down the hall to the TARDIS. He kept one hand on the wheelchair, helping to steer the Doctor in the right direction without actually assisting him. The TARDIS hadn't moved in the long year as she supported the paradox that allowed the Toclafane to come through. As they entered her the light was still red, even though Jack had destroyed the main part of the paradox machine. It was upon seeing her that the Doctor finally broke. He stood and stumbled up the ramp to the cage that surrounded her time router.

"No, no, no," he cried out as he clawed at the cage trying to take it down. His finger caught on a piece of the cage slicing it deep but the Doctor barely noticed as he continued to fight it.

"Sweetheart," Jack said softly in concern.

"I have to fix this. I can't leave her like this," The Doctor told Jack frantically. Jack wrapped his arms around the Doctor from behind and bit down softly on the claiming mark on his shoulder. The Doctor struggled against him as the tears began to fall. They streamed down his face as he sobbed.

"I've got you," Jack whispered against his shoulder. He nipped the mark again, not forcing the Doctor to submit but reminding him that he was claimed and loved by his Alpha. The Master had never touched his claiming mark after first biting him. Jack though made sure the Doctor knew that he was accepted as his mate. The Doctor went limp in Jack's arms and Jack carefully picked him up. He started to head towards the medi-bay, but the Doctor shook his head frantically.

"My room," He begged. He had enough of the medical wing when he was trapped by the Master.

"Are you sure?" Jack wondered as he looked at the Doctor.

"Please, Jack," The Doctor whimpered. Jack gave in and carried him to his bed. Laying him gently on it, he curled up beside the Doctor holding him. The Doctore continued to cry until exhaustion overtook him and he drifted off in Jack's arms. Jack held him long enough to be sure the Doctor was completely out before carefully getting out of bed. He went to the closet first, pulling out a pair of pajamas for the Doctor. Returning to the bed he removed the Doctor's shoes first before carefully unzipping the Doctor's trousers and slipping them down his legs. He let out a cry of horror before he was able to stop himself. How the Doctor was able to stand was beyond Jack as his legs were one black and blue bruise that started at his ankles and went up his thighs to almost his groin. They were criss-crossed with cuts and welts from whatever the Master had used to hit him.

"Oh sweetheart," Jack whispered. He forced himself to remain calm as he pulled on the pajama trousers and then helped the Doctor into the shirt. He tucked his lover into the soft duvet smiling as the Doctor sighed in content. After a year of sleeping on the floor or the hard medical bed, his mattress was a blessing. Jack didn't stick around to watch him sleep as he first went to the console room. He had planned on showering and climbing in bed with the Doctor but that was before he saw his legs. The cage came down as Jack took his anger out on the metal. His hands were bleeding and he had cut his arm but he took the pain and used it to make himself angrier. If the Master hadn't built the paradox machine in the first place, he wouldn't be bleeding, he decided. Finally, there was nothing left to destroy and he stepped back breathing hard. The lights in the room were still red as the TARDIS still needed a lot of work, but that would require the Doctor as Jack had no idea where to start.

Feeling better, he headed to the shower, washing the dust and grime off of his body. He dressed in his own pajamas but couldn't bring himself to go immediately back to the Doctor. Instead, he went in search of food. After a year of barely eating, he was literally starving. The Doctor of course didn't have food on the TARDIS and Jack didn't want to set foot on the Valiant again. Taking a deep breath, he made the choice to return to his lover. As he entered the Doctor's room he was surprised to see he was awake. He had curled on his side around a pillow, just holding it as he stared at the wall.

"How are you feeling?" Jack wondered as he sat down next to the Doctor.

"Lost," The Doctor replied. For months now he had pretended to be broken in order to save himself. Now that he could be a Beta again, he wasn't sure he wanted to.

"Oh sweetheart," Jack whispered. He leaned down and kissed the Doctor gently on the head. "You'll find your way again. We both will."

"Together?" The Doctor questioned, rolling his eyes over to look at Jack.

"If that is what you still want," Jack answered him. Jack had only claimed the Doctor to save him. If the Doctor didn't want him as an Alpha, Jack would understand eventually.

"It is. I want to travel again with you Jack and see the stars. Just you, me, and the baby?" The Doctor stated. He moved a protective hand to his stomach as he continued to stare at Jack.

"I will travel with you again, but I need to check on my team at Torchwood. During this year, I thought a lot about getting back to them. I also thought a lot about you and the baby. And I have to ask Doc, is it mine or his?" Jack asked. The Doctor's eyes narrowed.

"I don't know. I hope she is yours Jack, but I am not going to shun her if she is his. I have spent the last six months knowing she is growing inside of me, and loving her despite everything that happened. She didn't ask for this to happen. She is innocent and if you decided you don't want to help raise her because she turns out to be his, then you won't see me again," The Doctor informed Jack. "I won't have her growing up thinking she is wrong just because of who her father is."

"Even after all that he did to you, you still cared for him didn't you?" Jack wondered softly. He already knew the answer, but he wanted to hear it.

"He was once my best friend Jack. Koschei was once beautiful and if he hadn't given into his madness he could have done great things," The Doctor answered as he turned to look at the wall again. Taking a deep breath, Jack moved so that he was behind the Doctor. Laying down he placed one hand on the Doctor's stomach over the Doctor's hand.

"Then she will be beautiful as well," Jack whispered. He kissed the back of the Doctor's head and the Doctor smiled. It was harder for him to believe the words and he hoped the baby was his. Even if she wasn't, he would try to accept her. For his lover's sake.


	21. Chapter 21

The next day as they got the TARDIS ready to leave, was hard on them both. They had both spent the year under the Master's strict control and neither one of them knew how to get back to what was considered normal. Even though they had both watched the Master die there was still a sense of fear that he would appear again. That he would punish them for dismantling the paradox machine and moving about without his permission. There was also a general uneasiness between the Doctor and the Captain that may not have shown the day before but was clear the next morning.

It started simply enough. Jack had woken early and rolled out of bed. He still felt dirty from the long year so he first headed to the shower to try to wash the grim off his body. By the time he made it back to the room the Doctor was gone from the bed as well. Concerned due to the Doctor's pregnancy and the state of his legs, Jack went looking for him. Only to find the Doctor in the control room balancing on a bit of cage as he tried to get another piece out of the way so that he could get to the control panel.

"What are you doing," Jack cried out in alarm. Almost immediately the Doctor stepped off of the panel. In the same motion he dropped to his knees and into the submissive stance. His whole body was trembling in both fear and pain as he awaited his punishment.

"I was trying to fix the TARDIS, Alpha," The Doctor whispered, keeping his head as low as possible.

"No, don't do that," Jack told him as he moved over to help the Doctor up. The Doctor winced away from Jack's hand, not looking up. "I'm not going to hurt you, but I don't want you to submit to me either. I didn't mean to yell at you. You just startled me."

"I'm sorry," The Doctor whimpered. Jack knelt down in front of him and gently lifted the Doctor's chin. He looked straight into the large brown eyes of the Doctor. Leaning in he gently kissed him on the lips. The Doctor was still tense but relaxed as Jack continued to kneel in front of him. Slowly he unclasped his arms from behind his back and put them protectively over his stomach. Jack stood offering his hand to the Doctor once more and this time the Doctor allowed Jack to help him up.

"What do we need to do?" Jack questioned the Doctor. The Doctor pointed to a control panel that was blocked by the broken cage.

"I need to get into that panel and repair her circuits," The Doctor answered Jack. He moved back and allowed Jack to clear a path for him to get to the circuits. They didn't talk again as they both worked to restore the TARDIS. Jack cleared the control room of the cage and any other debris that was clutter her, while the Doctor took care of the finer details. Once she was able to safely achieve flight, he prepared to move her off of the Valiant and down to the Cardiff rift. There was one more thing he had to do first. Holding Jack's hand, they braved the Valiant one last time to retrieve the Master's body. It had been moved to the morgue and was set to be autopsied in the morning. The Doctor though couldn't allow that. With Jack's help he moved the Master's body into the medi-bay in the TARDIS. Once she was flight worthy, he would burn the body in the tradition of his people. For now though the Master would remain in cold storage. With the Master's body secured, he finally made the short jump to Cardiff. There was still a lot of work to be done before he could travel through space and time again for more than just a quick jump, but for now she could refuel while she was repaired.

"I don't know about you Doctor, but I am starving," Jack commented once they landed in Cardiff. "How about we take a break and have a late lunch?"

"I'm not hungry," The Doctor responded as he tried to disappear under the panel again. Jack put a hand on his arm to stop him.

"You need to eat and rest. You have been working nonstop since this morning and I know it has to be painful for you," Jack told him. Anger flashed in the Doctor's eyes for just a moment before he stared at Jack calmly.

"I don't need to rest or eat. I just need to get my life back," The Doctor stated firmly. He shook slightly as he knelt down in front of the panel again. Jack could see the tension in the Doctor's body as he awaited punishment for arguing with him.

"I'll make you a cuppa and a nice plate of chips, just in case you change your mind," Jack informed the Doctor. The Doctor nodded his thanks. He didn't relax though until Jack had stepped off of the TARDIS into the cool afternoon air. For half a moment, he contemplated closing the doors and locking Jack out. He shook his head and ran a hand down his stomach. His legs burned and his back was hurting him. Jack was right he was tired and he needed to eat. The fact that Jack had tried to order him to do so is what made him resist. Stubbornly he continued to work until after Jack had returned with his food. Then his body just couldn't take it anymore. He physically could not force himself to stand and Jack had to pick him up off of the TARDIS floor. He didn't look Jack in the eye as he was carried to his bed and tucked under the soft duvet.

"Do you need anything?" Jack wondered as he fought not to yell at the Doctor for his stupidity.

"My chips and tea please," The Doctor replied. Jack went back to the control room and retrieved the requested items. Setting them on the table beside the Doctor's bed, he left him alone for a minute. He couldn't continue to watch the Doctor hurt himself and he had no clue how to begin to help him or himself.


	22. Chapter 22

Jack didn't stay away from the Doctor long. Regardless of whether or not the Doctor was upsetting him, the need to protect his Omega was stronger. The last six months apart had hurt the bond that they had shared when during the first few months they had relied on each other to survive aboard the Valiant. Now they were almost two strangers once more. While the Doctor had been protected by the Master because of potentially carrying his child , Jack had not been so lucky. The last six months he had been chained in the room and been killed over and over again as the guards were allowed to release their anger on his body. Even if the Doctor had forgiven the Master, Jack knew that he never could.

Entering the Doctor's room, he found that he had barely touched his chips and the cup of tea had been allowed to cool. The Doctor was once more laying on his side staring at the wall. To see the Time Lord so lifeless worried Jack more then anything. The Doctor had always been hyperactive and on the move. A quiet Doctor was an unhappy Doctor and Jack could tell he was miserable.

"Not hungry after all?" Jack questioned as he looked at the uneaten food.

"No," The Doctor replied softly. Jack knelt beside the bed and took the Doctor's hand in his own. He brought it to his lips and kissed the inside of his wrist softly.

"That's alright you can eat later if you change your mind," Jack told him. The Doctor narrowed his eyes slightly as he turned and regarded Jack. Jack could see the suspicion clearly in them as he tried to figure out the game Jack was playing. Jack almost growled in frustration. The Doctor didn't want to be treated as an Omega but he clearly wasn't comfortable being treated as a Beta again. Jack would have even treated the Doctor as an Alpha if he thought it would help him. For once in his life Jack didn't know what to do. He had always acted on his instincts and drawn both women and men into his bed. This year had made himself doubt the man he was. If he was going to get Captain Jack back the first thing he had to do, as hard as it was, he was just going to have to trust his instincts again.

Closing his eyes he took a deep breath as he stood. He opened them again slowly and pushed aside the fact he was looking at the Doctor. The Omega laying in front of him was curled into himself, trying to protect his stomach, filled with an unknown Alpha's child. His legs though were separated slightly apart as the pressure from his wounds would make them ache. Moving his eyes up, he could clearly see that while the Doctor was holding the pillow, it was more to keep it near his body. The blankets, while not covering him, were also drawn tightly to his body. The Doctor's head was tilted slightly on the pillow almost unintentionally exposing the claiming mark that had been placed on his shoulder. Jack looked closer at the Doctor's eyes and while he was facing the wall, his eyes were actually looking downward, rather then at it. Everything about the way he was laying cried out to Jack that this Omega needed to submit.

Jack took another calming breath as he continued to stand near the bed. It seemed like hours had passed as he analyzed the Doctor when in reality only a few minutes had passed. Even if the Doctor had been raised to act like a Beta, he was still an Omega at heart. He had been pushed to follow his Omega instincts during the last six months and while he was fighting against them, he had been beat into submission by the Master. Jack could help him to be a beta once more, but first he had to help the Doctor rebuild his confidence and in doing so, hopefully rebuild his own. In order to do that he had to give the Doctor not necessarily what he wanted but what his body obviously needed.

"Jack?" The Doctor asked softly as Jack continued to stare at him. Jack didn't say anything but moved closer to the Doctor. Climbing on the bed, he moved the blankets out of the way and wrapped himself around the Doctor from behind. He pulled the Doctor's body as close to himself as possible, holding him tightly as he dared. The Doctor's breathing quickened slightly as Jack threw his leg over the Doctor's to pin him to the bed as he bit down on the claiming mark. The Doctor fought him, but Jack could tell it was more for show then the fact that he was trying to get away.

"Mine," Jack growled not releasing his shoulder. He held onto the Doctor until he went limp in his arms, giving into the Alpha holding him. Jack didn't release him as he slid his hand along the Doctor's body and pushed his fingers into the Doctor's trousers, sliding them across his bottom. The Doctor was slick and Jack celebrated silently that he had made the right call. Outwardly though, he made no acknowledgement then to move his hand out of the Doctor's trousers enough to pull them down. The Doctor trembled slightly in his arms as his bottom was exposed. Jack released his shoulder.

"I'm not going to hurt you," Jack promised. The Doctor nodded slightly.

"I trust you Alpha," He whispered. He turned his head towards Jack and Jack kissed him on the lips softly. He didn't force the kiss but allowed the Doctor to relax into it. As the Doctor opened his mouth slightly, Jack explored every corner of it with his tongue. He reached down and freed himself from his trousers. He ached with need and found himself thrusting against, but not entering the Doctor's body yet.

"I'm going to reclaim your body and then you will submit to no one else but me. Is that understood?" Jack asked him.

"Yes," The Doctor replied. The trembling had stopped and Jack slid easily into the willing body. The Doctor moaned as Jack kept his movements soft but deep. Their joining was slow as Jack reestablished himself as the Doctor's Alpha. He made sure thought that the Doctor found his release as well as he wasn't going to make the Doctor suffer anymore than he already had. As he felt himself nearing his own, he bit down on the Doctor's shoulder before allowing himself to fall over the edge. The Doctor cried out with both pain and pleasure before his body went limp again.

"Are you alright?" Jack asked in concern as the Doctor went still in his arms.

"Hmmm," The Doctor wondered. Jack sat up further to look into the Doctor's eyes. They were softer then before with the trust the Doctor had stated but not shown. Jack couldn't help the smile that crossed his face as he leaned down and kissed the Doctor again. He helped the Doctor pull up his trousers and then very carefully he eased himself out of the bed.

"I am going to make you a fresh cup of tea and get you a banana to eat. After you have eaten we are going to rest," Jack informed him making it clear it wasn't a request. The Doctor sat up so that he was leaning against the headboard. Jack hurried to retrieve the items and made it back to the Doctor's room quickly. The Doctor was still sitting on the bed and he didn't protest as Jack put the banana in his hand. Instead he opened it and lifted it to his mouth taking a bite. Jack climbed into the bed next to him, snuggling him close as he ate. The Doctor leaned into his touch, taking comfort in his Alpha.

"Jack," The Doctor said softly as he finished eating.

"Yes sweetheart?" Jack asked.

"Thank you," The Doctor told him. Jack held him tightly and kissed him on top of the head as the Doctor laid his head on Jack's chest. Listening to the sound of his Alpha's heart beating comforted him and soon he drifted off to sleep.


	23. Chapter 23

The Doctor woke up feeling warm, and comfortable in his bed. Jack was no longer in bed with him, but he had tucked the blankets tightly around him. For a moment, he almost panicked as he forgot where he was. The scent of his Alpha on the pillow reminded him though that he was in his room, safe aboard the TARDIS. It surprised the Doctor how much it comforted him to be restrained by Jack. When the Master had tried it, it had made him panic. With Jack though, he knew that being restrained meant comfort, not pain. For the first time in his long life, he found himself wanting to follow his Omega instincts. It was nice to step back and let someone else be in charge. He shuddered slightly as he thought of the Master forcing him to submit. Holding the pillow tighter, he forced his thoughts back to Jack.

Jack would never embarrass or hurt him. He could trust Jack to make the right decision while he didn't have to. He scolded himself softly for being a coward, but too many times in his 900 years he had to make life or death situations. Following his Omega instincts and letting Jack take control for awhile, or at least until after the baby was born, sounded like a better idea. The Doctor tried to decide if it was the hormones making him think like this or the fact for the first time in as far as he could remember he didn't have to fight against his natural urges.

His father would be ashamed if he could see his son submitting so easily. He would never forget the first time he had submitted. It had been right before his first heat. His father had been yelling at him for his grades. Without thinking about it, he had dropped to his knees and hung his head. His father had pulled him up roughly by his arm and walloped him.

"Alphas do not submit," his father had yelled. When he had gone into heat, he had expected to be punished for being an Omega. He had been on school holiday at the time when his body betrayed him presenting as an Omega. His father had drug him out to the barn and locked him inside of it as he tried to figure out what was happening. At school, they had been taught only females went into heat. He had suffered that week alone and scared, not realizing why his body ached the way it did. After his father wouldn't look at or acknowledge him. It was his mother who took him to the council and they put him on pills claiming him to be Beta. When they got home that evening his father had packed his clothes and he wad shipped back to the academy without so much as a goodbye.

Reaching up, he went to wipe away the tears that were starting to gather on his face. It was only then that he felt a slight tug on his arm. Opening his eyes for the first time, he saw the IV line in his wrist. Moving only his eyes, he followed the line up to the bag on the stand. There was about half a bag left. He furrowed his brow in unhappiness as he began to pick at the tape to remove the IV.

"Morning sleepy head. Why you leave that in place for now. I know you don't like IVs but you slept for 15 hours after barely eating or drinking the last few days. You were dehydrated and that is not good for you or our daughter," Jack told him softly as he noticed the Doctor was awake. He had been sitting by the bed keeping one eye on the Doctor as he tried to read a book. So far though he had accomplished reading the same paragraph several times and still had no idea what was happening in the story.

"It itches," The Doctor whined.

"No, it doesn't. You just want me to take it out and I will once you have more fluids in you. For now I need you to leave it in place," Jack told him a little more firmly. The Doctor nodded, but he looked at Jack with large sad eyes. Jack tried not to give in as his Omega was making him feel as though he had just told him that he would never see him again, rather than he needed the IV. Jack wasn't going to change his mind about it though. The Doctor had scared him to death when he had tried to wake him after eight hours of sleep and he couldn't wake him properly. Jack had examined him the best he could and then set up the IV. The Doctor had groaned and then curled up further into himself to continue sleeping.

"Good. Now how are you feeling?" Jack wondered.

"Thirsty," the Doctor answered after a moment.

"I can imagine. I will put the kettle on and I will get you a cuppa as soon as it is hot. Do you want a cup of water in the meantime?" Jack wondered. The Doctor scrunched his face at Jack. Jack laughed. "I didn't think so."

Jack left the room a moment to get the Doctor's tea and something for him to eat. There was still no food in the kitchen except for bananas. Sighing Jack grabbed two of them. After he was sure the Doctor was hydrated, he would see about taking him out for something to eat. Taking them and the cup of tea he went back to the Doctor's side. The Doctor had remained curled up in his bed and he grinned happily upon seeing the bananas. The Master had refused to give him bananas aboard the Valiant and he saw them as a perfectly acceptable meal. Sitting up he took the food from Jack. Jack didn't hand them over though until he had first kissed the Doctor softly.

"I love you," Jack told him as he broke the kiss. The Doctor didn't say it back but Jack understood as he crawled in bed with him, just to hold him once more. The three words were harder for him to say, and Jack understood that. As much as he wanted to hear it back, he didn't need to as the Doctor leaned against him, eating his bananas. He held him tightly, with one hand resting on the rounded stomach of his Omega. The baby was active and Jack could feel her kicking against his hand. It wasn't more than a slight bump at the moment, but the Doctor made a face as he looked down at his stomach.

"She wants to run already," The Doctor told Jack.

"Well she is your daughter," Jack informed him. The Doctor laughed. He finished his banana and cup of tea. He didn't argue as Jack checked him over, making sure that he was hydrated before removing the IV. He had decided he was going to submit to his Alpha and he meant it. Even when Jack suggested he shower before they finish the last of the repairs. After they could go pick Martha up for lunch. He had agreed and slunk to the shower when all he really wanted to do was lay in bed with Jack. Still he couldn't hide from the rest of the Universe forever. Could he?


	24. Chapter 24

The Doctor wasn't surprised when Martha didn't want to travel with him anymore. Though she said that she would see him again and that it had nothing to do with the fact that he really was an Omega, he didn't believe. He could see the difference in her eyes as she stared at him. She no longer looked at him with the respect of an Alpha towards a Beta, but down on him for his lower status. He kept his head held high though, not letting her make him feel weaker for being born an Omega. He had proven himself time and time again. There were people alive today because he had stepped up when no one else would.

"I want to take my pill again once the baby is born," The Doctor informed Jack once they were alone again in the TARDIS.

"Don't let Martha or anyone else make you feel as though you are not the man you were before this last year. You are just as strong without your pill as you are with it," Jack told him firmly.

"There will never be a time though when an Omega will be accepted as an Alpha. With my pill, I am able to hide my scent and help people. Without it, I am looked down upon. You may not care I am an Omega and other's may not mind as well, but those few that do can cause lives to be lost. I realized a long time ago that I can't run as an unclaimed Omega," The Doctor explained to Jack.

"You're claimed now though," Jack reminded him with a gentle nip on his shoulder.

"Jack." The Doctor drew out his name in annoyance.

"We will discuss it after the baby is born," Jack told him. The Doctor sighed but didn't continue to argue his Alpha. There was no point, especially when Jack pushed him gently down onto the Captain's chair and settled between his legs. The Doctor stared at Jack as his trousers were pulled down and thrown to the side.

"In the control room Alpha?" The Doctor admonished Jack with his tone as Jack pulled his own zipper down. His reply was Jack lifting his feet up onto his shoulders and pushing into his body.

"I waited a long time for this Doctor. I plan to claim you in almost every room aboard the TARDIS," Jack informed the Doctor as he started to move his hips. The Doctor reached back, grabbing the top of the Captain's chair to hold himself in place.

"You know that she is constantly changing and," he paused as he couldn't suppress the moan as Jack moved deeper. "And would take years to accomplish."

"Then it is a good thing you have a long life span and I am immortal," Jack replied. The Doctor opened his mouth to reply, but Jack took that moment to change his pace, so that he remained deep inside the Doctor's body. The Doctor threw his head back, as he grabbed tighter onto the seat. Jack couldn't help but smile to himself as he watched the Time Lord giving into the sensations that were bombarding his body. Not everyone could make the Time Lord go quiet and Jack was quite proud of himself for accomplishing it. He made the Doctor find his release first, then a second time before he finally followed him over the edge. By then the Doctor was limp in the chair, a sated, relaxed Time Lord. Jack chuckled as he picked him up in his arms and carried him back to their room.

-DW-

Over the next few months, life was quiet. The Doctor's stomach grew to the point that he had a slight waddle in his step as he made his way around the TARDIS. She was still parked on the rift as the Doctor didn't really feel like traveling much because when they did go on a trip, it was always to a safe planet. He yearned to run. He missed the rush of excitement as he had to run for his life for one reason or another. He knew it was safer for the baby if he didn't run, and Jack had called him insane for wanting to.

Maybe he wouldn't have wanted to run so badly if he hadn't been forced to be more domestic. Jack made sure that he had food aboard the TARDIS and he was expected to cook them actual meals. Jack ate dinner with him to make sure that he ate more than a banana for his evening meal. Then there was the fact that his TARDIS now had a complete nursery set up. The baby even had a cot in his room, bottles in the kitchen and a secured seat that could hold a car seat in the control room. Jack had put it in for them, for times the ride got a little bumpy. Well okay, it was always bumpy but it wasn't his fault that he was driving the TARDIS single handly when she was mean to be controlled by six people.

Jack had become overbearing the last few days as he quickly approached the end of his pregnancy. He was sitting alone in the library, just wanting five minutes alone, when he felt a strange wetness. Looking down, he could see that his trousers were soaked. He groaned loudly realizing that his water had broke. He was happy that the baby was finally coming but at the same time apprehensive. Her birth meant finally finding out who the father was. He would have happily raised her not knowing, but due to medications available, he had to find out. With the breaking of his water the contractions started. They ripped through his stomach, taking his breath away as he tried to block the pain.

"Jack," He cried out, no longer wanting to be alone, but desperately craving the touch of his Alpha. Jack rushed into the library. How he remained levelheaded, the Doctor wasn't sure. Jack though remained calm until after the contraction had subsided before leading him to the medi-bay. The Doctor wasn't happy to be back in it as he was stripped of his clothes.

"I am going to contact Martha and let her know you are in labor," Jack informed him. The Doctor nodded his head. They had discussed Jack delivering their daughter and Martha was only to come in if necessary. Jack had delivered his children in the past before modern medicine dictated that you went to the hospital. He was certain that he could deliver their daughter into the world as well.

The Doctor's labor was long and he writhed on the bed, never staying in one position for long as he tried to relieve the pain. He had refused pain medication wanting to give birth naturally. As the hours went on, Jack kept expecting him to give in. The Doctor never did though. Martha showed up after a while, to check on him. She still planned to let Jack actually deliver the baby, but she wanted to make sure the Doctor was doing alright. He was on his side as he went through another contraction and as soon as it was over, Martha carefully checked him.

"Jack it is time," She told him, moving out of the way to let Jack take over. "Doctor when I tell you to, you need to push."

"K," The Doctor whimpered. For the next short while his whole existence was centered around his stomach and Martha's encouragement to push. The relief he felt once the baby was out was nothing that he could have imagined. He listened to the wails of his daughter as Jack brought her up to his chest. Martha took Jack's place once more to clean him up as he focused on his tiny daughter. She had short brown hair and long fingers just like him. He kissed the top of her head, then kissed Jack.

"She's beautiful," Jack whispered.

"I love you so much little one," The Doctor told her as he kissed her again. Once she had fed for the first time, Martha took her to clean her up and weigh her. While she did, the Doctor asked Jack for a cup of tea. Jack left him alone a moment to retrieve it. Once he was alone the Doctor turned to Martha. "Can you please swab the inside of her cheek?"

Martha didn't question the Doctor as she did as he requested. She brought the swab over to him before leaving him alone once more. He pulled the monitor over to him and opened a tiny drawer on it. Within a moment, the TARDIS returned the DNA analysis. The Doctor smiled as he saw that his hopes had come true. The tiny bundle Martha was caring for was somehow Jacks. Jack returned to the room and the Doctor debated telling him.

"What?" Jack asked as he handed the Doctor his tea.

"Nothing. I am just happy she is here," The Doctor answered.


	25. Chapter 25

Jack sat beside the Doctor's bed as he took a well-deserved nap. In his arms was the tiny bundle that Jack would call his daughter, regardless of her bloodline. That didn't stop him from looking for any sign of whose daughter she truly was. The long fingers and brown hair told him nothing. She didn't have a cleft chin like him, but that didn't worry him. His brother didn't have one either due the genes in his family. Jack carefully moved the blanket and she cried her unhappiness about being exposed to the cold air.

"Does it really matter that much who her father is?" The Doctor asked. Jack looked up startled to see that the Doctor was watching him. He had been so focused on the baby in his arms that he didn't realize that the Doctor had woken up. "I mean that is what you are looking for. Any distinguishing mark or characteristic that would identify that she is yours or his."

"I can't help it, Doctor. I need to know," Jack told him honestly. The Doctor narrowed his eyes at Jack. Using the bed controls, he sat the bed up more and then reached for their daughter. Jack handed her to him. He watched as the Doctor held her close to him, snuggling her as he put his arms protectively around her, blocking her slightly from Jack's view. The gesture wasn't missed by Jack but when he opened his mouth to inform the Doctor he had no intention of hurting her, the Doctor interrupted him.

"Why do you need to know?" The Doctor wondered.

"You may not understand, but you chose me as your Alpha, long before I fought him and won that right. I swore to protect you, something that I failed at time and time again aboard the valiant," Jack began.

"It wasn't your fault," The Doctor informed him.

"It doesn't matter. Every time he hurt you, I felt like it was. After he broke our traditions and claimed you, he should have been killed. He only lived because you asked me not to kill him. Know that he claimed you hurts me, Doctor, and the fact that he could have bred you as well..." Jack went quiet for a moment taking a deep breath. Followed by another as he tried to regain his composer.

"The Master told me that if the baby was yours he would kill her. He couldn't get his answers while she was still in the womb and the fact that she has two hearts only confirms that she is my child as well. If we had failed to stop the Master I don't know how long it would have taken him to get his answer. The TARDIS could have easily confirmed that she is yours, but the Master had turned her into a paradox machine," The Doctor explained as he stared at Jack. He smiled as he saw Jack's eyes open slightly wider at his words.

"She's mine?" Jack asked in slight disbelief. The Doctor reached out to Jack turning the monitor towards him. He had the TARDIS display the baby's DNA results so that Jack could read them.

"I had hoped from the beginning that she was yours. A full Time Lord baby would have been the last of her kind. She is half Time Lord and Half human though making her the first of her kind. It should have been impossible but I have found out nothing is impossible with you Jack," The Doctor explained.

"The first of her kind?" Jack wondered. The Doctor nodded.

"And she will be beautiful."


End file.
